diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..de2aec7 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,148 @@ + + + + + + + + +Page not found (404) • rphenoscape + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 249be3b..7925794 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -8,21 +8,29 @@ License • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
@@ -68,7 +79,7 @@ -
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@@ -134,22 +145,32 @@

License

+ + + + + diff --git a/docs/articles/index.html b/docs/articles/index.html index 7082d7b..efafaf4 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -8,21 +8,29 @@ Articles • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
@@ -68,7 +79,7 @@ -
+
@@ -106,26 +117,31 @@

Articles

All vignettes

- +
+
RPhenoscape Intro
+
+
+ + + diff --git a/docs/articles/rphenoscape.html b/docs/articles/rphenoscape.html index 1443866..3cfbb61 100644 --- a/docs/articles/rphenoscape.html +++ b/docs/articles/rphenoscape.html @@ -6,18 +6,19 @@ RPhenoscape Intro • rphenoscape - - - + + + + + - - + - +
-

RPhenoscape Intro

+

RPhenoscape Intro

Hong Xu

@@ -83,59 +85,48 @@

Hong Xu

Installation

-

The development version of RPhenoscape is available on Github. It has not yet been released to [CRAN]. To install RPhenoscape from Github, use the install_github() function in the remotes package (which can be installed from CRAN using install.packages()). See the package README for details.

+

The development version of RPhenoscape is available on Github. It has not yet been released to [CRAN]. To install RPhenoscape from Github, use the install_github() function in the remotes package (which can be installed from CRAN using install.packages()). See the package README for details.

Once installed, the package can be loaded (“attached”) as any other R package:

-
library(rphenoscape)
+
+library(rphenoscape)

Character Matrix via OntoTrace

Use OntoTrace to obtain a character matrix for a taxonomic clade and anatomical region of interest.

The Phenoscape Knowledgebase web API returns the evolutionary character matrix in NeXML format. The first step is to get the NeXML object using pk_get_ontotrace_xml method.

-
nex <- pk_get_ontotrace_xml(taxon = c("Ictalurus", "Ameiurus"), entity = "fin spine")
+
+nex <- pk_get_ontotrace_xml(taxon = c("Ictalurus", "Ameiurus"), entity = "fin spine")

The result is an object of class nexml defined in the RNeXML package. The object mirrors the structure of a NeXML file, and can be inspected accordingly. Note that although generically NeXML files can contain multiple OTUs blocks and multiple characters blocks, NeXML files generated by the KB’s OntoTrace API contain only one. This means we can, for example, inspect the number of taxa and characters as follows:

-
# number of taxa in the first (and only) OTUs block
-length(nex@otus[[1]]@otu)
+
+# number of taxa in the first (and only) OTUs block
+length(nex@otus[[1]]@otu)
[1] 15
-
# number of characters in the first (and only) characters block
-length(nex@characters[[1]]@format@char)
+
+# number of characters in the first (and only) characters block
+length(nex@characters[[1]]@format@char)
[1] 2
-

More details on the nexml object can be found in the RNeXML documentation.

+

More details on the nexml object can be found in the RNeXML documentation.

Then retrieve wanted information from the NeXML object.
Get character matrix:

-
(m <- pk_get_ontotrace(nex))
-
                     taxa         otu
-1       Ameiurus brunneus VTO_0036273
-2          Ameiurus catus VTO_0036275
-3          Ameiurus melas VTO_0036272
-4        Ameiurus natalis VTO_0036274
-5      Ameiurus nebulosus VTO_0036278
-6  Ameiurus platycephalus VTO_0036276
-7   Ameiurus serracanthus VTO_0036277
-8     Ictalurus australis VTO_0061495
-9      Ictalurus balsanus VTO_0036221
-10      Ictalurus dugesii VTO_0061497
-11     Ictalurus furcatus VTO_0036223
-12        Ictalurus lupus VTO_0036220
-13    Ictalurus mexicanus VTO_0061498
-14       Ictalurus pricei VTO_0036218
-15    Ictalurus punctatus VTO_0036225
-                                    otus
-1  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-2  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-3  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-4  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-5  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-6  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-7  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-8  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-9  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-10 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-11 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-12 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-13 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-14 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-15 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
+
+(m <- pk_get_ontotrace(nex))

+
                     taxa         otu                                  otus
+1       Ameiurus brunneus VTO_0036273 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+2          Ameiurus catus VTO_0036275 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+3          Ameiurus melas VTO_0036272 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+4        Ameiurus natalis VTO_0036274 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+5      Ameiurus nebulosus VTO_0036278 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+6  Ameiurus platycephalus VTO_0036276 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+7   Ameiurus serracanthus VTO_0036277 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+8     Ictalurus australis VTO_0061495 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+9      Ictalurus balsanus VTO_0036221 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+10      Ictalurus dugesii VTO_0061497 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+11     Ictalurus furcatus VTO_0036223 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+12        Ictalurus lupus VTO_0036220 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+13    Ictalurus mexicanus VTO_0061498 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+14       Ictalurus pricei VTO_0036218 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+15    Ictalurus punctatus VTO_0036225 t7b654510-76d9-4b80-9e8c-00f72d1358b8
    anterior dentation of pectoral fin spine
 1                                         1
 2                                         1
@@ -169,7 +160,8 @@ 

 14                                               1
 15                                               1

 
The character matrix can be integrated with other data, such as meta data which include taxon identifiers, character identifiers, etc. Get meta data:

-
(meta <- pk_get_ontotrace_meta(nex))

+
+(meta <- pk_get_ontotrace_meta(nex))

 
$id_taxa
                     label                                       href
 1     Ictalurus mexicanus http://purl.obolibrary.org/obo/VTO_0061498
@@ -188,21 +180,21 @@ 

 14     Ictalurus balsanus http://purl.obolibrary.org/obo/VTO_0036221
 15      Ictalurus dugesii http://purl.obolibrary.org/obo/VTO_0061497
            otu                                  otus
-1  VTO_0061498 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-2  VTO_0036220 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-3  VTO_0036275 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-4  VTO_0036276 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-5  VTO_0036278 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-6  VTO_0061495 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-7  VTO_0036218 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-8  VTO_0036225 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-9  VTO_0036277 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-10 VTO_0036272 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-11 VTO_0036274 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-12 VTO_0036223 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-13 VTO_0036273 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-14 VTO_0036221 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-15 VTO_0061497 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
+1  VTO_0061498 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+2  VTO_0036220 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+3  VTO_0036275 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+4  VTO_0036276 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+5  VTO_0036278 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+6  VTO_0061495 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+7  VTO_0036218 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+8  VTO_0036225 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+9  VTO_0036277 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+10 VTO_0036272 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+11 VTO_0036274 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+12 VTO_0036223 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+13 VTO_0036273 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+14 VTO_0036221 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+15 VTO_0061497 t7b654510-76d9-4b80-9e8c-00f72d1358b8
 
 $id_entities
                                             label
@@ -217,13 +209,15 @@ 

 Character Matrices for Studies

 
To obtain the character matrices for studies published for a taxonomic clade and anatomical region of interest.

 
First step is to retrieve the list of studies given a taxonomic clade and anatomical structures (returned as data.frame).

-
(slist <- pk_get_study_list(taxon = "Ictalurus australis", entity = "fin"))

+
+(slist <- pk_get_study_list(taxon = "Ictalurus australis", entity = "fin"))

 
                                                                                                                                 id
 1 https://scholar.google.com/scholar?q=The+Phylogeny+of+Ictalurid+Catfishes%3A+A+Synthesis+of+Recent+Work&btnG=&hl=en&as_sdt=0%2C42
             label
 1 Lundberg (1992)

 
Based off the study ids retained from previous step, get the evolutionary character matrix for each study id (in NeXML-format) using pk_get_study_xml.

-
(nex_list <- pk_get_study_xml(slist$id))

+
+(nex_list <- pk_get_study_xml(slist$id))

 
$`https://scholar.google.com/scholar?q=The+Phylogeny+of+Ictalurid+Catfishes%3A+A+Synthesis+of+Recent+Work&btnG=&hl=en&as_sdt=0%2C42`
 A nexml object representing:
      0 phylogenetic tree block(s),  
@@ -232,24 +226,25 @@ 

         and  0 polymorphic or uncertain state(s) defined 
        matrix 1 has 22 row(s) 
      22 taxonomic units in 1 block(s) 
-  Taxa:  Ictalurus lupus, Ictalurus mexicanus, Ameiurus brunneus, Ictalurus furcatus, Trogloglanis pattersoni, Prietella phreatophila ...
+  Taxa:  Ictalurus pricei, Ictalurus lupus, Ameiurus natalis, Ameiurus nebulosus, Noturus insignis, Ictalurus australis ...
   Metadata annotations: 
     3 at top level 
     22 in block 1 at otu level 
-    0 in block 1 at char level 
-    367 in block 1 at state level
+    115 in block 1 at char level 
+    734 in block 1 at state level
 
 NeXML generated by RNeXML using schema version: 0.9 
-Size: 6.6 Mb 

+Size: 7.3 Mb 

 
From the list of NeXML objects, retrieve the character matrices.

-
study_matrix <- pk_get_study(nex_list)
-study_matrix[[1]][1:5, 1:5]

+
+study_matrix <- pk_get_study(nex_list)
+study_matrix[[1]][1:5, 1:5]

 
                taxa                                      otu
-1  Ameiurus brunneus otu_0214da59-b8c7-4918-b79d-7ef8082d7828
-2     Ameiurus catus otu_1373ce68-22c2-46fe-b90c-b899cf2906db
-3     Ameiurus melas otu_1494afe7-7913-4f07-bb4d-326a647c4fc9
-4   Ameiurus natalis otu_e14d634c-4e1a-4d41-b968-7d7d9a7d0bca
-5 Ameiurus nebulosus otu_e8b32b67-f2d0-4b80-8470-19007745953b
+1  Ameiurus brunneus otu_905bdcf6-5e27-4f66-9961-a34e81b03140
+2     Ameiurus catus otu_65e45284-e2fd-4867-a53e-36475b267e2f
+3     Ameiurus melas otu_ca02c929-3632-49d9-8564-df319184a5a5
+4   Ameiurus natalis otu_34dd3fce-8268-43b5-af73-df184afc8f4d
+5 Ameiurus nebulosus otu_9916d34b-9b21-4292-95b2-ac550e495c3a
   Anal-fin rays, species mean count Anterior dentations of pectoral spine
 1                           16.1-20                                 large
 2                         20.1-25.5                              moderate
@@ -263,78 +258,79 @@ 

 4              3-6 moderately sharp serrae
 5               <3 moderately sharp serrae

 
Each character matrix can be integrated with other data, such as meta data which include taxon identifiers, character identifiers, etc. Get meta data:

-
study_metas <- pk_get_study_meta(nex_list)
-study_metas[[1]]

+
+study_metas <- pk_get_study_meta(nex_list)
+study_metas[[1]]

 
$id_taxa
                      label                                       href
-1          Ictalurus lupus http://purl.obolibrary.org/obo/VTO_0036220
-2      Ictalurus mexicanus http://purl.obolibrary.org/obo/VTO_0061498
-3        Ameiurus brunneus http://purl.obolibrary.org/obo/VTO_0036273
-4       Ictalurus furcatus http://purl.obolibrary.org/obo/VTO_0036223
-5  Trogloglanis pattersoni http://purl.obolibrary.org/obo/VTO_0061501
-6   Prietella phreatophila http://purl.obolibrary.org/obo/VTO_0036265
-7      Ictalurus punctatus http://purl.obolibrary.org/obo/VTO_0036225
-8      Pylodictis olivaris http://purl.obolibrary.org/obo/VTO_0036282
-9   Ameiurus platycephalus http://purl.obolibrary.org/obo/VTO_0036276
-10        Ameiurus natalis http://purl.obolibrary.org/obo/VTO_0036274
-11     Ictalurus australis http://purl.obolibrary.org/obo/VTO_0061495
-12   Ameiurus serracanthus http://purl.obolibrary.org/obo/VTO_0036277
-13          Noturus flavus http://purl.obolibrary.org/obo/VTO_0036263
-14       Ictalurus dugesii http://purl.obolibrary.org/obo/VTO_0061497
-15        Ictalurus pricei http://purl.obolibrary.org/obo/VTO_0036218
-16        Satan eurystomus http://purl.obolibrary.org/obo/VTO_0061485
-17        Noturus insignis http://purl.obolibrary.org/obo/VTO_0036237
-18      Ameiurus nebulosus http://purl.obolibrary.org/obo/VTO_0036278
-19       Noturus stigmosus http://purl.obolibrary.org/obo/VTO_0036261
-20      Ictalurus balsanus http://purl.obolibrary.org/obo/VTO_0036221
-21          Ameiurus melas http://purl.obolibrary.org/obo/VTO_0036272
-22          Ameiurus catus http://purl.obolibrary.org/obo/VTO_0036275
+1         Ictalurus pricei http://purl.obolibrary.org/obo/VTO_0036218
+2          Ictalurus lupus http://purl.obolibrary.org/obo/VTO_0036220
+3         Ameiurus natalis http://purl.obolibrary.org/obo/VTO_0036274
+4       Ameiurus nebulosus http://purl.obolibrary.org/obo/VTO_0036278
+5         Noturus insignis http://purl.obolibrary.org/obo/VTO_0036237
+6      Ictalurus australis http://purl.obolibrary.org/obo/VTO_0061495
+7      Ictalurus mexicanus http://purl.obolibrary.org/obo/VTO_0061498
+8   Prietella phreatophila http://purl.obolibrary.org/obo/VTO_0036265
+9           Ameiurus melas http://purl.obolibrary.org/obo/VTO_0036272
+10     Pylodictis olivaris http://purl.obolibrary.org/obo/VTO_0036282
+11      Ictalurus furcatus http://purl.obolibrary.org/obo/VTO_0036223
+12       Ictalurus dugesii http://purl.obolibrary.org/obo/VTO_0061497
+13        Satan eurystomus http://purl.obolibrary.org/obo/VTO_0061485
+14  Ameiurus platycephalus http://purl.obolibrary.org/obo/VTO_0036276
+15      Ictalurus balsanus http://purl.obolibrary.org/obo/VTO_0036221
+16   Ameiurus serracanthus http://purl.obolibrary.org/obo/VTO_0036277
+17          Noturus flavus http://purl.obolibrary.org/obo/VTO_0036263
+18       Noturus stigmosus http://purl.obolibrary.org/obo/VTO_0036261
+19     Ictalurus punctatus http://purl.obolibrary.org/obo/VTO_0036225
+20          Ameiurus catus http://purl.obolibrary.org/obo/VTO_0036275
+21       Ameiurus brunneus http://purl.obolibrary.org/obo/VTO_0036273
+22 Trogloglanis pattersoni http://purl.obolibrary.org/obo/VTO_0061501
                                         otu
-1  otu_7fdb78b4-9591-4d71-b1ea-e9e1865f035e
-2  otu_282f9f9a-8a51-44c0-a4ea-e44e4a543782
-3  otu_0214da59-b8c7-4918-b79d-7ef8082d7828
-4  otu_f08ec6dc-0700-42cd-935f-a54e9d759581
-5  otu_bc0bce0e-76ca-40f3-870e-08b7576db2c3
-6  otu_8c13c6ef-0e46-436b-bb29-286f4bab7773
-7  otu_3b7971e0-c5a9-4a28-813c-c2fa28e77e8e
-8  otu_7fb806e7-e50d-4aec-a44b-3a1a696a73ae
-9  otu_a65b02e8-afdd-4270-9e53-a444561ac50c
-10 otu_e14d634c-4e1a-4d41-b968-7d7d9a7d0bca
-11 otu_0033c0e1-33ba-4d97-9899-b6d709023412
-12 otu_e40c3a11-59eb-422a-8e9a-4781504874a7
-13 otu_10e67bb2-7d72-47d2-97c0-4753fadcf7c1
-14 otu_027d8dcc-e3f0-4c7d-b604-cbf371af27f0
-15 otu_4b1ae5c5-6380-4064-b738-ea88380176f5
-16 otu_7fdc2286-ce03-4167-85f5-215b6d886a31
-17 otu_b00bc531-3d3b-49ff-9c7c-9949aa2767ea
-18 otu_e8b32b67-f2d0-4b80-8470-19007745953b
-19 otu_9991f0e8-cfcf-4348-9034-056516c99b3c
-20 otu_91221715-1aec-4a9e-9813-6bfdbef5fa1a
-21 otu_1494afe7-7913-4f07-bb4d-326a647c4fc9
-22 otu_1373ce68-22c2-46fe-b90c-b899cf2906db
+1  otu_ad5e6e49-2a9e-43e8-af87-3016bd16cd35
+2  otu_e473e64d-055e-4364-8022-2158dc2a523e
+3  otu_34dd3fce-8268-43b5-af73-df184afc8f4d
+4  otu_9916d34b-9b21-4292-95b2-ac550e495c3a
+5  otu_8b30cd95-359c-4a54-a2fd-72002b9ff0d4
+6  otu_ce8050ad-493d-494b-ac73-508917b9207a
+7  otu_3aebb08b-5385-476e-a2fd-dc356c0606dd
+8  otu_c2e9a6a8-6582-4249-8836-7597ae6cc9e6
+9  otu_ca02c929-3632-49d9-8564-df319184a5a5
+10 otu_df074a9c-9fd4-433d-80a5-70211a534348
+11 otu_2cf53956-e59a-4c22-a625-ebd0f5e1b7e5
+12 otu_3a012267-3f5d-44e2-91b3-d5e0e10bbcbe
+13 otu_2dbc0322-7fe9-4d13-9c14-64818e24cc24
+14 otu_08b57892-301f-4c1b-91a5-1349949be25f
+15 otu_7bad6a92-00b9-41e4-a357-6c29fb74dfc6
+16 otu_bb9223d2-a342-464f-83e0-25fdbd76865c
+17 otu_b54b9416-f054-4879-8f64-62d446c87c85
+18 otu_e309e6a6-2c40-4271-9296-85b11a8dad2a
+19 otu_ee040977-66bc-4b65-b3ea-a036131c096c
+20 otu_65e45284-e2fd-4867-a53e-36475b267e2f
+21 otu_905bdcf6-5e27-4f66-9961-a34e81b03140
+22 otu_7b401d3e-4732-4c59-9e21-df0d9a5e406a
                                         otus
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 $id_entities
                                                               label
@@ -454,121 +450,121 @@ 

 114                                                   Pelvic splint
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+99  character_6b088f13-2efd-4757-a51a-5b4851273432
+100 character_4a6f5266-e4aa-4537-9a30-bb2f79225018
+101 character_92a1f1f9-a6e0-41b7-86fd-d3d426ea55c0
+102 character_a40cf987-fe21-4d33-8617-1daf43210649
+103 character_2df39fe7-99f0-4d8c-a7f6-7e01f5ba60e3
+104 character_611956a4-0533-4a82-bba5-1258f5b5bc25
+105 character_a32f71ec-0bb1-46c1-bd20-07237bf0e2bf
+106 character_91733b6c-3381-4ab5-8b0c-62bc85ae3f86
+107 character_538ea3ca-6401-4086-84c2-54fdf47288d4
+108 character_3d6c610f-25e6-4689-bb9e-5e59a017ac6f
+109 character_baede3f1-f154-46b1-be5a-0c35e90c5a3e
+110 character_bcda4da1-0738-4de9-be68-23db5d16e8a6
+111 character_00c5b8d1-7dc2-454c-84e2-5ae44070c3c9
+112 character_98af142a-4863-4384-bbe3-f77e0a8705b5
+113 character_b11abedc-1302-458d-b44b-147e55e58f26
+114 character_5f591638-fff4-409b-bfe3-74cb3396bece
+115 character_bc73b575-e7fb-4d8f-8f8d-fc6dc6be2f21

@@ -577,39 +573,24 @@

Subsetting a Matrix

A matrix obtained from Phenoscape can be subsetted (filtered) by taxonomic subgroup or anatomical part. For example, using pk_is_descendant and pk_is_ancestor methods, a matrix can be subsetted to a taxonomic subgroup that is the descendants/ancestors of a given taxon.

-
m # original character matrix
-
                     taxa         otu
-1       Ameiurus brunneus VTO_0036273
-2          Ameiurus catus VTO_0036275
-3          Ameiurus melas VTO_0036272
-4        Ameiurus natalis VTO_0036274
-5      Ameiurus nebulosus VTO_0036278
-6  Ameiurus platycephalus VTO_0036276
-7   Ameiurus serracanthus VTO_0036277
-8     Ictalurus australis VTO_0061495
-9      Ictalurus balsanus VTO_0036221
-10      Ictalurus dugesii VTO_0061497
-11     Ictalurus furcatus VTO_0036223
-12        Ictalurus lupus VTO_0036220
-13    Ictalurus mexicanus VTO_0061498
-14       Ictalurus pricei VTO_0036218
-15    Ictalurus punctatus VTO_0036225
-                                    otus
-1  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-2  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-3  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-4  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-5  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-6  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-7  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-8  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-9  tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-10 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-11 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-12 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-13 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-14 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-15 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
+
+m # original character matrix

+
                     taxa         otu                                  otus
+1       Ameiurus brunneus VTO_0036273 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+2          Ameiurus catus VTO_0036275 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+3          Ameiurus melas VTO_0036272 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+4        Ameiurus natalis VTO_0036274 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+5      Ameiurus nebulosus VTO_0036278 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+6  Ameiurus platycephalus VTO_0036276 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+7   Ameiurus serracanthus VTO_0036277 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+8     Ictalurus australis VTO_0061495 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+9      Ictalurus balsanus VTO_0036221 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+10      Ictalurus dugesii VTO_0061497 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+11     Ictalurus furcatus VTO_0036223 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+12        Ictalurus lupus VTO_0036220 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+13    Ictalurus mexicanus VTO_0061498 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+14       Ictalurus pricei VTO_0036218 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+15    Ictalurus punctatus VTO_0036225 t7b654510-76d9-4b80-9e8c-00f72d1358b8
    anterior dentation of pectoral fin spine
 1                                         1
 2                                         1
@@ -642,19 +623,21 @@ 

 13                                               1
 14                                               1
 15                                               1

-
(is_desc <- pk_is_descendant('Ictalurus', m$taxa))

-
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE
-[12]  TRUE  TRUE  TRUE  TRUE

-
m[is_desc, ] #subsetting to the descendants of Ictalurus

+
+(is_desc <- pk_is_descendant('Ictalurus', m$taxa))

+
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
+[13]  TRUE  TRUE  TRUE

+
+m[is_desc, ] #subsetting to the descendants of Ictalurus

 
                  taxa         otu                                  otus
-8  Ictalurus australis VTO_0061495 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-9   Ictalurus balsanus VTO_0036221 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-10   Ictalurus dugesii VTO_0061497 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-11  Ictalurus furcatus VTO_0036223 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-12     Ictalurus lupus VTO_0036220 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-13 Ictalurus mexicanus VTO_0061498 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-14    Ictalurus pricei VTO_0036218 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
-15 Ictalurus punctatus VTO_0036225 tdd52b01a-3c48-4c89-8410-1ddd16530fe1
+8  Ictalurus australis VTO_0061495 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+9   Ictalurus balsanus VTO_0036221 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+10   Ictalurus dugesii VTO_0061497 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+11  Ictalurus furcatus VTO_0036223 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+12     Ictalurus lupus VTO_0036220 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+13 Ictalurus mexicanus VTO_0061498 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+14    Ictalurus pricei VTO_0036218 t7b654510-76d9-4b80-9e8c-00f72d1358b8
+15 Ictalurus punctatus VTO_0036225 t7b654510-76d9-4b80-9e8c-00f72d1358b8
    anterior dentation of pectoral fin spine
 8                                         1
 9                                         0
@@ -678,15 +661,17 @@ 

 

 Term Search

 
Search for details for a given taxon:

-
pk_taxon_detail("Coralliozetus")

+
+pk_taxon_detail("Coralliozetus")

 
                                          id         label extinct
 1 http://purl.obolibrary.org/obo/VTO_0042955 Coralliozetus   FALSE
                                          rank.id rank.label common_name
 1 http://purl.obolibrary.org/obo/TAXRANK_0000005      genus        <NA>

 
Search for details for a given anatomical structure:

-
pk_anatomical_detail("basihyal bone")

-
          label
-1 basihyal bone
+
+pk_anatomical_detail("basihyal bone")

+
          label                               isDefinedBy
+1 basihyal bone http://purl.obolibrary.org/obo/uberon.owl
                                                                                 definition
 1 Replacement bone that is median and is the anterior-most bone of the ventral hyoid arch.
                                              id
@@ -695,12 +680,15 @@ 

 

 Miscellaneous methods:

 
Resolve a given term to its IRI:

-
pk_get_iri("Coralliozetus", "vto")

+
+pk_get_iri("Coralliozetus", "vto")

 
[1] "http://purl.obolibrary.org/obo/VTO_0042955"

-
pk_get_iri("basihyal bone", "uberon")

+
+pk_get_iri("basihyal bone", "uberon")

 
[1] "http://purl.obolibrary.org/obo/UBERON_0011618"

 
Test if a taxon is extinct:

-
pk_is_extinct("Fisherichthys")

+
+pk_is_extinct("Fisherichthys")

 
Fisherichthys 
          TRUE
@@ -708,33 +696,29 @@

- +
-

Developed by Hong Xu, Hilmar Lapp.

+

Developed by Hong Xu, Hilmar Lapp, John Bradley.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.6.1.

+
+ diff --git a/docs/authors.html b/docs/authors.html index 7ce38d6..62c6b4b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -8,21 +8,29 @@ Authors • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
@@ -68,7 +79,7 @@ -
+
@@ -108,7 +119,11 @@

Authors

  • -

    Hilmar Lapp. Maintainer, author. ORCID +

    Hilmar Lapp. Maintainer, author. +

    +
    • +
  • +

    John Bradley. Author.

    • @@ -118,19 +133,23 @@

    Authors

    +
    + + diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $(''); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
  • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/index.html b/docs/index.html index 43b04a0..72e376b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -5,11 +5,13 @@ -Semantically rich phenotypic traits from the Phenoscape Knowledgebase • rphenoscape - - - - +Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase • rphenoscape + + + + + + - - -
    + +
    -
    - - - - +
    +

    RPhenoscape: Semantically rich phenotypic traits from the Phenoscape Knowledgebase

      -
    • Author: Hong Xu, Hilmar Lapp
      • +
    • Author: Hong Xu, Hilmar Lapp, John Bradley
    • Maintainer: Hilmar Lapp
    -

    Most of the services provided with the Phenoscape Knowledgebase web API return data in JSON format, plain text (usually tab-delimited), and NeXML. This package facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, retrieving term info, and querying data matrices.

    +

    Most of the services provided with the Phenoscape Knowledgebase API return data in JSON format, plain text (usually tab-delimited), and NeXML. This package facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, retrieving term info, and querying data matrices.

    Installation

    -

    The development version of RPhenoscape is available on Github. It has not yet been released to CRAN. To install RPhenoscape from Github, use the install_github() function in the remotes package (which can be installed from CRAN using install.packages()):

    -
    remotes::install_github("phenoscape/rphenoscape")
    +

    The development version of RPhenoscape is available on Github. It has not yet been released to CRAN. To install RPhenoscape from Github, use the install_github() function in the remotes package (which can be installed from CRAN using install.packages()):

    +
    +remotes::install_github("phenoscape/rphenoscape")

    By default, this will skip building the package vignettes. To build and install package vignettes as well, you must have recent versions of the knitr and rmarkdown packages installed, and use additional parameters, depending on the version of the remotes package you have installed, to request building vignettes.

    -
    packageVersion("remotes")
    -
    [1] '2.0.4'
    +
    +packageVersion("remotes")
    +
    [1] '2.1.1'

    If the version is 2.1.0 or higher, use the build_vignettes parameter (which by default is FALSE):

    -
    remotes::install_github("phenoscape/rphenoscape", build_vignettes = TRUE)
    +
    +remotes::install_github("phenoscape/rphenoscape", build_vignettes = TRUE)

    If the version of remotes is lower, use the build_opts parameter:

    -
    remotes::install_github("phenoscape/rphenoscape", build_opts=c("--no-manual"))
    +
    +remotes::install_github("phenoscape/rphenoscape", build_opts=c("--no-manual"))

    Once installed, the package can be loaded (“attached”) as any other R package:

    -
    library(rphenoscape)
    +
    +library(rphenoscape)

    @@ -116,17 +118,18 @@

  • Subsetting matrices by taxonomic subgroup or anatomical part
  • Searching for details for a given taxon
    • +

    By definition, most functions in this package connect to the Phenoscape Knowledgebase API. The base URL path to the API endpoints can changed from the default by setting the PHENOSCAPE_API environment variable. (See R Startup and RStudio support on .Renviron on how to control environment variables at R session startup.)

    Phenoscape Knowledgebase

    - + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c03fb08..1273238 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -17,12 +17,14 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; flex-direction: column; - - padding-top: 60px; } body > .container .row { @@ -69,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -102,37 +108,135 @@ a.anchor { margin-top: -40px; } -/* Static header placement on mobile devices */ -@media (max-width: 767px) { - .navbar-fixed-top { - position: absolute; - } - .navbar { - padding: 0; - } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; } +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} /* Sidebar --------------------------*/ -#sidebar { +#pkgdown-sidebar { margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; } -#sidebar h2 { + +#pkgdown-sidebar h2 { font-size: 1.5em; margin-top: 1em; } -#sidebar h2:first-child { +#pkgdown-sidebar h2:first-child { margin-top: 0; } -#sidebar .list-unstyled li { +#pkgdown-sidebar .list-unstyled li { margin-bottom: 0.5em; } +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { - height: 16px; + font-size: 16px; + color: #A6CE39; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; vertical-align: middle; } @@ -140,14 +244,14 @@ a.anchor { .ref-index th {font-weight: normal;} -.ref-index td {vertical-align: top;} +.ref-index td {vertical-align: top; min-width: 100px} .ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} .ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} .ref-arguments .name {width: 20%;} .ref-arguments .desc {width: 80%;} @@ -222,6 +326,19 @@ a.sourceLine:hover { visibility: visible; } +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + /* mark.js ----------------------------*/ mark { @@ -234,3 +351,17 @@ mark { .html-widget { margin-bottom: 10px; } + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index eb7e83d..7e7048f 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,18 +2,11 @@ (function($) { $(function() { - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); - }); + $('.navbar-fixed-top').headroom(); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); }); $('[data-toggle="tooltip"]').tooltip(); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e158a6b..58579c2 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,9 @@ pandoc: 1.19.2.1 -pkgdown: 1.3.0 +pkgdown: 1.6.1 pkgdown_sha: ~ articles: rphenoscape: rphenoscape.html +last_built: 2021-03-31T19:31Z urls: reference: http://rphenoscape.phenoscape.org/reference article: http://rphenoscape.phenoscape.org/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png new file mode 100644 index 0000000..17a3580 Binary files /dev/null and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/add_provenance_record.html b/docs/reference/add_provenance_record.html index ffd8514..f63e358 100644 --- a/docs/reference/add_provenance_record.html +++ b/docs/reference/add_provenance_record.html @@ -8,21 +8,29 @@ Generate and add provenance record to nexml — add_provenance_record • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,13 +38,13 @@ - + - + @@ -50,9 +58,10 @@ + - +
    @@ -74,7 +83,7 @@ -
    +
    @@ -111,16 +120,14 @@

    Generate and add provenance record to nexml

    -

    If the content of a nexml object is modified, this function can add a provenance record documenting the modification. The provenance documentation is added to the toplevel metadata (i.e., at the "nexml" level).

    -
    - 
    add_provenance_record(nexml, cmd = NA, creator = Sys.getenv("USER"))
    - + 
    add_provenance_record(nexml, cmd = NA, creator = Sys.getenv("USER"))
    +

    Arguments

    @@ -141,11 +148,10 @@

    Arg software. The default is the system's USER environment variable.

    - +

    Value

    A nexml object with provenance records added.

    -

    Details

    At present, for each invocation this implementation will do the following:

      @@ -177,35 +183,33 @@

      Details ] .

    - -
    - +
    +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/anatomy_ontology_iris.html b/docs/reference/anatomy_ontology_iris.html index 42eb877..ff14469 100644 --- a/docs/reference/anatomy_ontology_iris.html +++ b/docs/reference/anatomy_ontology_iris.html @@ -8,21 +8,29 @@ Get IRIs of ontologies with anatomy terms — anatomy_ontology_iris • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,13 +38,13 @@ - + - + @@ -50,9 +58,10 @@ + - +
    @@ -74,7 +83,7 @@ -
    +
    @@ -111,45 +120,44 @@

    Get IRIs of ontologies with anatomy terms

    -

    Obtains the IRIs of anatomical entity ontologies in the Phenoscape KB. Note that this will normally include the Gene Ontology (GO), because it contains a substantial number of anatomical entity terms in its subcellular location branch.

    -
    - 
    anatomy_ontology_iris()
    - + 
    anatomy_ontology_iris()
    + +

    Value

    A character vector

    -
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/corpus_size.html b/docs/reference/corpus_size.html index 61a3e04..94162a1 100644 --- a/docs/reference/corpus_size.html +++ b/docs/reference/corpus_size.html @@ -8,21 +8,29 @@ Obtain the size of different corpora — corpus_size • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -72,7 +81,7 @@ -
    +
    @@ -109,15 +118,13 @@

    Obtain the size of different corpora

    -

    Obtains the size of a certain number of predefined corpora. The total size of a corpus is important for calculating term frequencies.

    -
    - 
    corpus_size(corpus = c("taxon_annotations", "taxa", "gene_annotations",
-  "genes"))
    - + 
    corpus_size(corpus = c("taxon_annotations", "taxa", "gene_annotations",
+  "genes"))
    +

    Arguments

    @@ -129,49 +136,45 @@

    Arg acceptable.

    - +

    Value

    the size of the specified corpus as an integer number.

    -

    Details

    Corpus sizes are cached per session after they have first been obtained. Thus, if the Phenoscape KB changes, a session needs to be restarted to have those changes be reflected.

    -

    Examples

    - 
    corpus_size("taxa")
    #> [1] 752
    corpus_size("taxon_annotations")
    #> [1] 805354
    + 
    corpus_size("taxa")
+
    #> [1] 785
    corpus_size("taxon_annotations")
+
    #> [1] 809892
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/find_term.html b/docs/reference/find_term.html index 6fee2f5..d278a29 100644 --- a/docs/reference/find_term.html +++ b/docs/reference/find_term.html @@ -8,21 +8,29 @@ Find terms matching a query text — find_term • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -72,7 +81,7 @@ -
    +
    @@ -109,16 +118,14 @@

    Find terms matching a query text

    -

    Searches the KB for terms matching the given text, and returns the result(s) as a data frame (see Value).

    -
    - 
    find_term(query, type = NA, definedBy = quote(!is.na(.)),
-  matchBy = NA, matchTypes = NA, nomatch = NA, limit = 100,
-  verbose = FALSE)
    - + 
    find_term(query, type = NA, definedBy = quote(!is.na(.)),
+  matchBy = NA, matchTypes = NA, nomatch = NA, limit = 100,
+  verbose = FALSE)
    +

    Arguments

    @@ -148,13 +155,13 @@

    Arg to match. Provide as IRIs or using common namespace prefixes. The default is NA, which will use the remote API's default, currently "rdfs:label", "oboInOwl:hasExactSynonym", "oboInOwl:NarrowSynonym", and -"oboInOwl:hasBroadSynonym". To match only against label, use c("rdfs:label").

    +"oboInOwl:hasBroadSynonym". To match only against label, use c("rdfs:label").

    +Use c("exact") to accept exact matches only.

    @@ -171,46 +178,42 @@

    Arg

    matchTypes

    character, the types of matches (exact, partial, broad) to accept. By default (value NA), no filtering by match type is performed. -Use c("exact") to accept exact matches only.
    nomatch

    logical; whether to issue a message if no matches found
    - +

    Value

    A data frame with columns "id", "label", "isDefinedBy", and "matchType" and one row for each term match.

    -

    Details

    Matches can be filtered by type of term (class, property, etc), ontology in which the term is defined, and by type of match (exact, partial, etc). The term properties considered for matching can also be controlled.

    - - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/get_KBinfo.html b/docs/reference/get_KBinfo.html index 13a96f7..e60a3af 100644 --- a/docs/reference/get_KBinfo.html +++ b/docs/reference/get_KBinfo.html @@ -8,21 +8,29 @@ Summary and metadata about the Phenoscape KB — get_KBinfo • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -72,7 +81,7 @@ -
    +
    @@ -109,17 +118,15 @@

    Summary and metadata about the Phenoscape KB

    -

    Returns the date of the current release of the Phenoscape Knowledgebase (KB) and counts of annotated matrices, taxa, phenotypes, characters, and states.

    -
    - 
    get_KBinfo()
+    
    get_KBinfo()
 
 # S3 method for KBinfo
-print(x, ..., tz = "")
    
-    
+print(x, ..., tz = "")
    +

    Arguments

    @@ -138,48 +145,47 @@

    Arg local timezone

    - +

    Value

    A list of class "KBinfo" with summary statistics of annotation counts and other KB metadata (specifically, a timestamp for the current KB build).

    -

    Examples

    - 
    kbmeta <- get_KBinfo()
-names(kbmeta)
    #> [1] "annotated_taxa"       "annotated_characters" "annotated_matrices"  
-#> [4] "annotated_states"     "build_time"          
    kbmeta
    #> Annotated taxa: 6118
-#> Annotated characters: 12724
-#> Annotated matrices: 217
-#> Annotated states: 26407
-#> Build time: 2019-12-03 15:19:58 EST
    + 
    kbmeta <- get_KBinfo()
+names(kbmeta)
+
    #> [1] "annotated_taxa"       "annotated_characters" "annotated_matrices"  
+#> [4] "annotated_states"     "build_time"          
    kbmeta
+
    #> Annotated taxa: 6206
+#> Annotated characters: 13364
+#> Annotated matrices: 230
+#> Annotated states: 26905
+#> Build time: 2020-04-08 16:37:21 EDT
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/get_data.html b/docs/reference/get_data.html index cbc4472..9341056 100644 --- a/docs/reference/get_data.html +++ b/docs/reference/get_data.html @@ -8,21 +8,29 @@ Get data from an API endpoint — get_data • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -72,7 +81,7 @@ -
    +
    @@ -109,18 +118,17 @@

    Get data from an API endpoint

    -

    Obtains and parses data from JSON, CSV, and NeXML-returning API endpoints, respectively.

    -
    - 
    get_json_data(url, query, verbose = FALSE, ensureNames = NULL)
+    
    get_json_data(url, query, verbose = FALSE, ensureNames = NULL,
+  forceGET = FALSE)
+
+get_csv_data(url, query, ..., verbose = FALSE, forceGET = FALSE)
 
-get_csv_data(url, query, ..., verbose = FALSE)
+get_nexml_data(url, query, verbose = FALSE, forceGET = FALSE)
    
 
-get_nexml_data(url, query, verbose = FALSE)
    -

    Arguments

    @@ -141,53 +149,56 @@

    Arg

    + + + + +read.csv()

    character, which column or list names to ensure are included in the result to be returned. If result returned by the API endpoint does not include them, they will be added, with NA values.

    forceGET

    logical, whether to force using the HTTP GET method for API +access regardless of request length. The default is FALSE, meaning queries +exceeding a certain size for transmission will automatically use HTTP POST +for accessing the KB API.
    ...

    for get_csv_data, additional parameters to be passed on to -read.csv()
    - +

    Value

    For get_json_data, a data frame or list, depending on the result of -jsonlite::fromJSON().

    +jsonlite::fromJSON().

    For get_csv_data, a data frame.

    For get_nexml_data, a nexml object.

    -

    Details

    These are package-internal functions.

    - - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/get_phenotypes.html b/docs/reference/get_phenotypes.html index 2e16f4e..bb18fdf 100644 --- a/docs/reference/get_phenotypes.html +++ b/docs/reference/get_phenotypes.html @@ -8,21 +8,29 @@ Retrieve phenotypes by entity, quality, taxon, and study — get_phenotypes • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,14 +38,14 @@ - + - + @@ -51,9 +59,10 @@ + - +
    @@ -75,7 +84,7 @@ -
    +
    @@ -112,18 +121,16 @@

    Retrieve phenotypes by entity, quality, taxon, and study

    -

    Retrieves "semantic phenotypes", i.e., phenotypes encoded as ontological expressions. Filtering is possible by anatomical entity (optionally including entities related by certain properties, see includeRels), phenotypic quality, taxonomic group where the phenotypes have been recorded, and study (a.k.a. publication).

    -
    - 
    get_phenotypes(entity = NA, quality = NA, taxon = NA, study = NA,
-  includeRels = c("part of"), .withTaxon = FALSE, verbose = FALSE)
    - + 
    get_phenotypes(entity = NA, quality = NA, taxon = NA, study = NA,
+  includeRels = c("part of"), .withTaxon = FALSE, verbose = FALSE)
    +

    Arguments

    @@ -167,7 +174,7 @@

    Arg time-consuming operations. Default is FALSE.

    - +

    Value

    A data frame with columns "id" and "label".

    @@ -176,82 +183,77 @@

    Value

    (phenotypes, taxon) tuples will be unique, both phenotypes and taxa individually will then be redundant in the returned data frame (the association is n:n).

    -

    Details

    Entity, quality, and taxon can be given as IRI or as name (i.e, term label). In the latter case, names will be resolved to IRIs against anatomy ontologies, PATO, and taxonomy ontologies, respectively. Warnings will be issued if only a partial match can be found. The study must be given as IRI.

    -

    Examples

    - 
    # NOT RUN {
-phens1 <- get_phenotypes(entity = "pelvic fin")
-head(phens1)
+    
    if (FALSE) {
+phens1 <- get_phenotypes(entity = "pelvic fin")
+head(phens1)
 
 # by default, parts are already included
-phens2 <- get_phenotypes(entity = "pelvic fin", includeRels = c("part"))
-nrow(phens1) == nrow(phens2)
-table(phens2$id %in% phens1$id)
+phens2 <- get_phenotypes(entity = "pelvic fin", includeRels = c("part"))
+nrow(phens1) == nrow(phens2)
+table(phens2$id %in% phens1$id)
 
 # but historical homologues are not
-phens2 <- get_phenotypes(entity = "pelvic fin", includeRels = c("part", "hist"))
-table(phens2$id %in% phens1$id)
+phens2 <- get_phenotypes(entity = "pelvic fin", includeRels = c("part", "hist"))
+table(phens2$id %in% phens1$id)
 
 # neither are serially homologous
-phens2 <- get_phenotypes(entity = "pelvic fin", includeRels = TRUE)
-table(phens2$id %in% phens1$id)
+phens2 <- get_phenotypes(entity = "pelvic fin", includeRels = TRUE)
+table(phens2$id %in% phens1$id)
 
 # filter also by quality
-phens2 <- get_phenotypes(entity = "pelvic fin", quality = "shape")
-table(phens1$id %in% phens2$id)
+phens2 <- get_phenotypes(entity = "pelvic fin", quality = "shape")
+table(phens1$id %in% phens2$id)
 
 # filter also by quality and taxon
-phens2 <- get_phenotypes(entity = "pelvic fin", quality = "shape", taxon = "Siluriformes")
-table(phens1$id %in% phens2$id)
+phens2 <- get_phenotypes(entity = "pelvic fin", quality = "shape", taxon = "Siluriformes")
+table(phens1$id %in% phens2$id)
 
 # filter by entity, quality and taxon, and return taxa as well (resulting in
 # (phenotype, taxon) "tuples")
-phens2a <- get_phenotypes(entity = "pelvic fin", quality = "shape", taxon = "Siluriformes",
-                          .withTaxon = TRUE)
-head(phens2a)
-nrow(phens2a) - nrow(phens2) # lots of redundancy due to n:n relationship
-nrow(unique(phens2a[,c("id", "label")])) == nrow(phens2) # but same #phenotypes
+phens2a <- get_phenotypes(entity = "pelvic fin", quality = "shape", taxon = "Siluriformes",
+                          .withTaxon = TRUE)
+head(phens2a)
+nrow(phens2a) - nrow(phens2) # lots of redundancy due to n:n relationship
+nrow(unique(phens2a[,c("id", "label")])) == nrow(phens2) # but same #phenotypes
 
 # can compute and visualize similarity
-sm <- jaccard_similarity(terms = phens2$id, .labels = phens2$label, .colnames = "label")
-plot(hclust(as.dist(1-sm)))
-# }
    
+sm <- jaccard_similarity(terms = phens2$id, .labels = phens2$label, .colnames = "label")
+plot(hclust(as.dist(1-sm)))
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/get_term_label.html b/docs/reference/get_term_label.html index b4c82c5..2d325bc 100644 --- a/docs/reference/get_term_label.html +++ b/docs/reference/get_term_label.html @@ -8,21 +8,29 @@ Obtains the labels for a list of terms — get_term_label • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -73,7 +82,7 @@ -
    +
    @@ -110,15 +119,13 @@

    Obtains the labels for a list of terms

    -

    Attempts to obtain the label for each term, identified by IRI, in the input list. Terms for which no label is found in the database will have NA as the label in the result (see Value).

    -
    - 
    get_term_label(term_iris, preserveOrder = FALSE, verbose = FALSE)
    - + 
    get_term_label(term_iris, preserveOrder = FALSE, verbose = FALSE)
    +

    Arguments

    @@ -138,39 +145,38 @@

    Arg time-consuming operations.

    - +

    Value

    A data.frame with columns "id" and "label". The "id" column contains the IRIs. The label will be NA for term IRIs that are not present in the KB, or for which the KB cannot produce a label.

    - - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 9b20bfa..5601196 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -8,21 +8,29 @@ Function reference • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,12 @@ + + @@ -44,9 +54,10 @@ + - +
    @@ -68,7 +79,7 @@ -
    +
    @@ -117,6 +128,11 @@

    + + + + + @@ -314,27 +330,30 @@

    -

    Contents

    -     +

    +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/nexml_drop.html b/docs/reference/nexml_drop.html index 76036dc..1fa7463 100644 --- a/docs/reference/nexml_drop.html +++ b/docs/reference/nexml_drop.html @@ -8,21 +8,29 @@ Drop parts of a nexml object — nexml_drop • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,8 +38,8 @@ - + - + @@ -62,9 +70,10 @@ + - +
    @@ -86,7 +95,7 @@ -
    +
    @@ -123,11 +132,10 @@

    Drop parts of a nexml object

    -

    nexml_drop_otu drops OTUs (taxa) from a nexml object. Currently none of the OTUs to be dropped can be used in a tree that's part of the nexml object. If they are, first drop the OTUs from the tree(s) -(for example, using drop.tip() from package "ape"), then +(for example, using drop.tip() from package "ape"), then replace the tree(s). Dropping OTUs will not only drop them from the OTUs block, but will also drop matrix rows that referenced the OTUs to be dropped. This may in turn leave some characters unused. Therefore, it is recommended @@ -140,18 +148,17 @@

    Drop parts of a nexml object

    unused characters.

    is_unused_otu is a filter function for nexml_drop_otu for dropping unused OTUs.

    -
    - 
    nexml_drop_otu(nexml, filter, at = NA, block = 1, ...)
+    
    nexml_drop_otu(nexml, filter, at = NA, block = 1, ...)
+
+nexml_drop_char(nexml, filter, at = NA, block = 1, ...,
+  pruneStates = TRUE, pruneRows = TRUE)
 
-nexml_drop_char(nexml, filter, at = NA, block = 1, ...,
-  pruneStates = TRUE, pruneRows = TRUE)
+is_unused_char(charList, ...)
 
-is_unused_char(charList, ...)
+is_unused_otu(otuList, ...)
    
 
-is_unused_otu(otuList, ...)
    -

    Arguments

    @@ -218,7 +225,7 @@

    Arg to filter on.

    - +

    Value

    The functions for dropping components return a nexml @@ -230,12 +237,12 @@

    Value

    object that is not used in either the matrix (or matrices) of the characters block(s), or, unless ignoreTrees = TRUE, for a node of a tree, and FALSE otherwise.

    -

    Examples

    - 
    nex <- RNeXML::nexml_read(system.file("examples", "ontotrace-result.xml", package = "rphenoscape"))
+    
    nex <- RNeXML::nexml_read(system.file("examples", "ontotrace-result.xml", package = "rphenoscape"))
 # drop by label matching
-nexml_drop_otu(nex, filter = function(x) grepl(" sp.", x), at = "label")
    #> A nexml object representing:
+nexml_drop_otu(nex, filter = function(x) grepl(" sp.", x), at = "label")
+
    #> A nexml object representing:
 #>  	 1 phylogenetic tree block(s), where:
 #> 	   block 1 contains 0 phylogenetic tree(s) 
 #>  	 1 character block(s), where:
@@ -260,15 +267,15 @@ 
    Examp
 #> NeXML generated by RNeXML using schema version: 0.9 
 #> Size: 209.6 Kb 
    
 # can pipe dropping and then removing potentially unused characters or OTUs:
-library(dplyr)
    #> 
-#> Attaching package: ‘dplyr’
    #> The following object is masked from ‘package:testthat’:
-#> 
-#>     matches
    #> The following objects are masked from ‘package:stats’:
+library(dplyr)
+
    #> 
+#> Attaching package: ‘dplyr’
    #> The following objects are masked from ‘package:stats’:
 #> 
 #>     filter, lag
    #> The following objects are masked from ‘package:base’:
 #> 
-#>     intersect, setdiff, setequal, union
    nexml_drop_char(nex, filter = function(x) grepl("pelvic", x), at = "label") %>%
-  nexml_drop_otu(filter = is_unused_otu)
    #> A nexml object representing:
+#>     intersect, setdiff, setequal, union
    nexml_drop_char(nex, filter = function(x) grepl("pelvic", x), at = "label") %>%
+  nexml_drop_otu(filter = is_unused_otu)
+
    #> A nexml object representing:
 #>  	 1 phylogenetic tree block(s), where:
 #> 	   block 1 contains 0 phylogenetic tree(s) 
 #>  	 1 character block(s), where:
@@ -294,48 +301,47 @@ 
    Examp
 #> 
 #> NeXML generated by RNeXML using schema version: 0.9 
 #> Size: 205.8 Kb 
    
-
    # NOT RUN {
-nex <- pk_get_ontotrace_xml(taxon = "Ictaluridae",
-                            entity = "fin", variable_only = FALSE)
+if (FALSE) {
+nex <- pk_get_ontotrace_xml(taxon = "Ictaluridae",
+                            entity = "fin", variable_only = FALSE)
 # ontotrace results store VTO IRIs in dwc:taxonID annotations:
-nexml_drop_otu(nex,
-               filter = function(x) !pk_is_descendant("Ictalurus", x),
-               at = "dwc:taxonID") %>%
-  nexml_drop_char(filter = is_unused_char)
+nexml_drop_otu(nex,
+               filter = function(x) !pk_is_descendant("Ictalurus", x),
+               at = "dwc:taxonID") %>%
+  nexml_drop_char(filter = is_unused_char)
 # anatomy IRIs are in obo:IAO_0000219 ("denotes") annotations:
-nexml_drop_char(nex,
-               filter = function(x)
-                 !pk_is_descendant("paired fin", x, includeRels = "part_of"),
-               at = "obo:IAO_0000219") %>%
-  nexml_drop_otu(filter = is_unused_otu)
-# }
    
+nexml_drop_char(nex,
+               filter = function(x)
+                 !pk_is_descendant("paired fin", x, includeRels = "part_of"),
+               at = "obo:IAO_0000219") %>%
+  nexml_drop_otu(filter = is_unused_otu)
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/obo_prefix.html b/docs/reference/obo_prefix.html index 8f16504..59fabdd 100644 --- a/docs/reference/obo_prefix.html +++ b/docs/reference/obo_prefix.html @@ -8,21 +8,29 @@ Extract the OBO ontology prefix from IRIs — obo_prefix • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,13 +117,11 @@

    Extract the OBO ontology prefix from IRIs

    -

    Extract the OBO ontology prefix from IRIs

    -
    - 
    obo_prefix(x)
    - + 
    obo_prefix(x)
    +

    Arguments

    @@ -123,48 +130,46 @@

    Arg

    a list or vector of IRIs, and/or objects that have an "id" key.
    - +

    Value

    A character vector of the same length as the input vector or list, with NA in the positions where extracting the OBO ontology prefix failed.

    -

    Examples

    - 
    tt <- c("http://purl.obolibrary.org/obo/UBERON_0011618",
+    
    tt <- c("http://purl.obolibrary.org/obo/UBERON_0011618",
         "http://purl.obolibrary.org/obo/PATO_0002279",
         "http://purl.obolibrary.org/obo/VTO_0071642",
         "http://purl.obolibrary.org/obo/MP_0030825",
-        "http://purl.obolibrary.org/obo/NCBITaxon_7955")
-obo_prefix(tt)
    #> [1] "UBERON"    "PATO"      "VTO"       "MP"        "NCBITaxon"
    
+        "http://purl.obolibrary.org/obo/NCBITaxon_7955")
+obo_prefix(tt)
+
    #> [1] "UBERON"    "PATO"      "VTO"       "MP"        "NCBITaxon"
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pa_dep_matrix.html b/docs/reference/pa_dep_matrix.html index 353bd04..e4010f5 100644 --- a/docs/reference/pa_dep_matrix.html +++ b/docs/reference/pa_dep_matrix.html @@ -8,21 +8,29 @@ Obtains a presence-absence dependency matrix — pa_dep_matrix • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,8 +38,8 @@ - + - + @@ -53,9 +61,10 @@ + - +
    @@ -77,7 +86,7 @@ -
    +
    @@ -114,7 +123,6 @@

    Obtains a presence-absence dependency matrix

    -

    Obtains a presence-absence dependency matrix for the given set of terms. The resulting matrix M will have values 1 and 0, where M[i,j] = 1 iff the presence if term i implies the presence of term j. Note that it follows that @@ -122,12 +130,11 @@

    Obtains a presence-absence dependency matrix

    Note also that the matrix is asymmetric; that is, M[i,j] = 1 does not imply M[j,i] = 1 for \(i\neq j\). Terms i and j (\(i\neq j\)) for which M[i,j] = M[j,i] = 1 are sometimes referred to as super-dependent.

    -
    - 
    pa_dep_matrix(terms, .names = c("ID", "IRI", "label"), .labels = NULL,
-  preserveOrder = FALSE, verbose = FALSE)
    - + 
    pa_dep_matrix(terms, .names = c("ID", "IRI", "label"), .labels = NULL,
+  preserveOrder = FALSE, verbose = FALSE)
    +

    Arguments

    @@ -168,7 +175,7 @@

    Arg potentially time-consuming operations.

    - +

    Value

    A data.fram M with M[i,j] = 1 iff the presence of term i implies the @@ -180,51 +187,49 @@

    Value

    have attribute term.iris, giving the term IRIs for the rows (and columns). Note that these extra attributes will be lost upon subsetting the returned matrix.

    -

    Examples

    - 
    # NOT RUN {
-tl <- c("http://purl.obolibrary.org/obo/UBERON_0000981",
+    
    if (FALSE) {
+tl <- c("http://purl.obolibrary.org/obo/UBERON_0000981",
         "http://purl.obolibrary.org/obo/UBERON_0002103",
         "http://purl.obolibrary.org/obo/UBERON_0000976",
-        "http://purl.obolibrary.org/obo/UBERON_0002102")
-m <- pa_dep_matrix(tl)
-m # term IDs as row and column names
-id_prefixes <- attr(m, "prefixes")
-id_prefixes # 4x "http://purl.obolibrary.org/obo/"
-
-m <- pa_dep_matrix(tl, .names = "label")
-m # term labels as row and column names
-mat_terms <- attr(m, "term.iris")
-mat_terms # term IRIs in the same order as rows (and columns)
-# }
    
+        "http://purl.obolibrary.org/obo/UBERON_0002102")
+m <- pa_dep_matrix(tl)
+m # term IDs as row and column names
+id_prefixes <- attr(m, "prefixes")
+id_prefixes # 4x "http://purl.obolibrary.org/obo/"
+
+m <- pa_dep_matrix(tl, .names = "label")
+m # term labels as row and column names
+mat_terms <- attr(m, "term.iris")
+mat_terms # term IRIs in the same order as rows (and columns)
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/phenotype.html b/docs/reference/phenotype.html index dcf85b9..2ec58df 100644 --- a/docs/reference/phenotype.html +++ b/docs/reference/phenotype.html @@ -8,21 +8,29 @@ Phenotype Objects — phenotype • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,8 +38,8 @@ - + - + @@ -60,9 +68,10 @@ + - +
    @@ -84,7 +93,7 @@ -
    +
    @@ -121,7 +130,6 @@

    Phenotype Objects

    -

    as.phenotype creates an object (or a list of objects) of type "phenotype". The object to be coerced can be a character vector (of IRIs), or a data.frame. In the latter case, there must be a column "id" with the IRIs of phenotypes. @@ -136,25 +144,24 @@

    Phenotype Objects

    chars extracts the (non-redundant) characters from the phenotype object (or an object coercible to phenotype).

    print pretty-prints objects of type "phenotype"

    -
    - 
    as.phenotype(x, withTaxa = FALSE, ...)
+    
    as.phenotype(x, withTaxa = FALSE, ...)
 
 # S3 method for data.frame
-as.phenotype(x, ...)
+as.phenotype(x, ...)
 
-is.phenotype(x)
+is.phenotype(x)
 
-is_valid_phenotype(x)
+is_valid_phenotype(x)
 
-charstates(x)
+charstates(x)
 
-chars(x)
+chars(x)
 
 # S3 method for phenotype
-print(x, ...)
    
-    
+print(x, ...)
    +

    Arguments

    @@ -174,7 +181,7 @@

    Arg

    additional parameters where applicable; ignored for printing
    - +

    Value

    as.phenotype returns and object of type "phenotype", or a list of such objects @@ -202,18 +209,19 @@

    Value

    chars returns a data.frame with collumns "character.id" and "character.label" (IRI and label of the character), and "study.id" and "study.label" (IRI and short label for the study to which the character and state belong).

    -

    Details

    Create and test objects of type "phenotype", and extract properties from them.

    -

    Examples

    # query for a set of phenotypes (IDs and their labels)
-phens <- get_phenotypes(entity = "basihyal bone")
-nrow(phens)
    #> [1] 19
    # turn one into a phenotype object
-obj <- as.phenotype(phens[3, "id"])
-class(obj)
    #> [1] "phenotype" "list"     
    obj
    #> Phenotype 'basihyal bone absent'
+phens <- get_phenotypes(entity = "basihyal bone")
+nrow(phens)
+
    #> [1] 20
    # turn one into a phenotype object
+obj <- as.phenotype(phens[3, "id"])
+class(obj)
+
    #> [1] "phenotype" "list"     
    obj
+
    #> Phenotype 'basihyal bone absent'
 #> Linked to states:
 #>                label character.label           study.label
 #> 1  states 0, 1 and 2        Basihyal Imamura et al. (2005)
@@ -230,7 +238,8 @@ 
    Examp
 #> 
 #> No information about taxa exhibiting this phenotype.
    
 # optionally include taxa exhibiting the phenotype
-as.phenotype(phens[3,], withTaxa = TRUE)
    #> Phenotype 'basihyal bone absent'
+as.phenotype(phens[3,], withTaxa = TRUE)
+
    #> Phenotype 'basihyal bone absent'
 #> Linked to states:
 #>                label character.label           study.label
 #> 1  states 0, 1 and 2        Basihyal Imamura et al. (2005)
@@ -252,7 +261,8 @@ 
    Examp
 #> 4 http://purl.obolibrary.org/obo/VTO_0052740   Hemitripterus villosus
 #> 5 http://purl.obolibrary.org/obo/VTO_0052539        Liparis agassizii
 #>  [ reached 'max' / getOption("max.print") -- omitted 6 rows ]
    # full list of taxa:
-as.phenotype(phens[3,], withTaxa = TRUE)$taxa
    #>                                            id                      label
+as.phenotype(phens[3,], withTaxa = TRUE)$taxa
+
    #>                                            id                      label
 #> 1  http://purl.obolibrary.org/obo/VTO_0035423          Corydoras rabauti
 #> 2  http://purl.obolibrary.org/obo/VTO_0052870          Enophrys diceraus
 #> 3  http://purl.obolibrary.org/obo/VTO_0071753   Eumicrotremus asperrimus
@@ -265,8 +275,12 @@ 
    Examp
 #> 10 http://purl.obolibrary.org/obo/VTO_0034991               Siluriformes
 #> 11 http://purl.obolibrary.org/obo/VTO_0036124             Silurus glanis
    
 # can also coerce entire list at once
-objs <- as.phenotype(phens)
-class(objs)
    #> [1] "list"
    length(objs)
    #> [1] 19
    all(sapply(objs, is.phenotype))
    #> [1] TRUE
    objs[[3]]
    #> Phenotype 'basihyal bone absent'
+objs <- as.phenotype(phens)
+class(objs)
+
    #> [1] "list"
    length(objs)
+
    #> [1] 20
    all(sapply(objs, is.phenotype))
+
    #> [1] TRUE
    objs[[3]]
+
    #> Phenotype 'basihyal bone absent'
 #> Linked to states:
 #>                label character.label           study.label
 #> 1  states 0, 1 and 2        Basihyal Imamura et al. (2005)
@@ -283,86 +297,76 @@ 
    Examp
 #> 
 #> No information about taxa exhibiting this phenotype.
    
 # extract character states and (non-redundant) characters
-charstates(obj)
    #>                                                                     id
-#> 1 http://purl.org/phenoscape/uuid/aad2b9ab-d755-41c3-b0d4-07828af709bd
-#> 2 http://purl.org/phenoscape/uuid/d432b4d8-f351-40bc-8dde-bf14aaa1cbd1
-#> 3 http://purl.org/phenoscape/uuid/302e3faf-9ac3-40c7-936a-047249b3c8cf
-#> 4 http://purl.org/phenoscape/uuid/559715cf-1fcf-48e0-bd5f-0f4d3f06fded
+charstates(obj)
+
    #>                                                                     id
+#> 1 http://purl.org/phenoscape/uuid/62b5a920-8b49-42be-86f9-baab28a601fc
+#> 2 http://purl.org/phenoscape/uuid/eb9a3385-bd7f-46a8-ac8f-ac109e8e0e3c
+#> 3 http://purl.org/phenoscape/uuid/78fa240f-904b-4018-89e9-07c1550539fc
+#> 4 http://purl.org/phenoscape/uuid/5b7b3d47-890a-4bf7-be90-61417c3d1bf3
 #>                label
 #> 1  states 0, 1 and 2
 #> 2 absent (unordered)
 #> 3             Absent
 #> 4    basihyal absent
 #>                                                           character.id
-#> 1 http://purl.org/phenoscape/uuid/1d8251ad-2454-4d7a-8b59-f4a425332003
-#> 2 http://purl.org/phenoscape/uuid/1d8251ad-2454-4d7a-8b59-f4a425332003
-#> 3 http://purl.org/phenoscape/uuid/6a9cc2f1-88c0-419a-8bca-0bb3918e7bb0
-#> 4 http://purl.org/phenoscape/uuid/b54a1da4-4e8f-4495-8c29-6a05d4d7c6bb
-#>   character.label
-#> 1        Basihyal
-#> 2        Basihyal
-#> 3   Basihyal bone
-#> 4        Basihyal
-#>                                                                                                                                                                          study.id
-#> 1                                                                                                                                     http://dx.doi.org/10.1007/s10228-005-0282-6
-#> 2                                                                                                                                     http://dx.doi.org/10.1007/s10228-005-0282-6
-#> 3                                                                                            http://specifyassets.nhm.ku.edu/Ichthyology/originals/sp68693518805352821487.att.pdf
-#> 4 https://scholar.google.com/scholar?q=Higher-level+Phylogeny+of+Siluriformes%2C+With+a+New+Classification+of+the+Order+%28Teleostei%2C+Ostariophysi%29&btnG=&hl=en&as_sdt=0%2C42
+#> 1 http://purl.org/phenoscape/uuid/44a9193e-4da7-45ba-9eae-6ca060579da2
+#> 2 http://purl.org/phenoscape/uuid/44a9193e-4da7-45ba-9eae-6ca060579da2
+#> 3 http://purl.org/phenoscape/uuid/46cd66db-2454-4304-bf12-9a63aa7421ba
+#> 4 http://purl.org/phenoscape/uuid/cedb8568-c69e-45b1-907c-d9a0bc677f6e
+#>   character.label                                    study.id
+#> 1        Basihyal http://dx.doi.org/10.1007/s10228-005-0282-6
+#> 2        Basihyal http://dx.doi.org/10.1007/s10228-005-0282-6
+#> 3   Basihyal bone http://dx.doi.org/10.11646/zootaxa.2877.1.1
+#> 4        Basihyal      https://ci.nii.ac.jp/naid/10012505149/
 #>             study.label
 #> 1 Imamura et al. (2005)
 #> 2 Imamura et al. (2005)
 #> 3  Mabee et al.  (2011)
-#> 4       De Pinna (1993)
    chars(obj)
    #>                                                           character.id
-#> 1 http://purl.org/phenoscape/uuid/1d8251ad-2454-4d7a-8b59-f4a425332003
-#> 3 http://purl.org/phenoscape/uuid/6a9cc2f1-88c0-419a-8bca-0bb3918e7bb0
-#> 4 http://purl.org/phenoscape/uuid/b54a1da4-4e8f-4495-8c29-6a05d4d7c6bb
-#>   character.label
-#> 1        Basihyal
-#> 3   Basihyal bone
-#> 4        Basihyal
-#>                                                                                                                                                                          study.id
-#> 1                                                                                                                                     http://dx.doi.org/10.1007/s10228-005-0282-6
-#> 3                                                                                            http://specifyassets.nhm.ku.edu/Ichthyology/originals/sp68693518805352821487.att.pdf
-#> 4 https://scholar.google.com/scholar?q=Higher-level+Phylogeny+of+Siluriformes%2C+With+a+New+Classification+of+the+Order+%28Teleostei%2C+Ostariophysi%29&btnG=&hl=en&as_sdt=0%2C42
+#> 4       De Pinna (1993)
    chars(obj)
+
    #>                                                           character.id
+#> 1 http://purl.org/phenoscape/uuid/44a9193e-4da7-45ba-9eae-6ca060579da2
+#> 3 http://purl.org/phenoscape/uuid/46cd66db-2454-4304-bf12-9a63aa7421ba
+#> 4 http://purl.org/phenoscape/uuid/cedb8568-c69e-45b1-907c-d9a0bc677f6e
+#>   character.label                                    study.id
+#> 1        Basihyal http://dx.doi.org/10.1007/s10228-005-0282-6
+#> 3   Basihyal bone http://dx.doi.org/10.11646/zootaxa.2877.1.1
+#> 4        Basihyal      https://ci.nii.ac.jp/naid/10012505149/
 #>             study.label
 #> 1 Imamura et al. (2005)
 #> 3  Mabee et al.  (2011)
 #> 4       De Pinna (1993)
    
-
    # NOT RUN {
+if (FALSE) {
 # IDs that don't resolve still yield an object, but is not valid
-obj <- as.phenotype("http://foo")
-is.phenotype(obj)
-is_valid_phenotype(obj)
-# }
    +obj <- as.phenotype("http://foo") +is.phenotype(obj) +is_valid_phenotype(obj) +} + - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/phenotype_matches.html b/docs/reference/phenotype_matches.html index 07a9955..aad2514 100644 --- a/docs/reference/phenotype_matches.html +++ b/docs/reference/phenotype_matches.html @@ -8,21 +8,29 @@ Which phenotypes match filter — phenotype_matches • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,13 +117,11 @@

    Which phenotypes match filter

    -

    Determines which of one or more phenotype IDs match the given filter.

    -
    - 
    phenotype_matches(x, studies)
    - + 
    phenotype_matches(x, studies)
    +

    Arguments

    @@ -129,52 +136,48 @@

    Arg is allowed if it has a column labeled "id".

    - +

    Value

    a logical vector of the same length as the vector of phenotypes, with TRUE as element if the corresponding phenotype matches, and FALSE otherwise.

    -

    Details

    At present, the only supported query filter is a list of studies (as their IDs). A phenotype matches if it is linked to at least one of the studies.

    -

    Examples

    - 
    x <- get_phenotypes(entity = "basihyal bone")
-nrow(x)
    #> [1] 19
    # which of these are in the same study or studies as the first one?
-phenotype_matches(x, pk_get_study_list(phenotype = x$id[1]))
    #>  [1]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
-#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE
    + 
    x <- get_phenotypes(entity = "basihyal bone")
+nrow(x)
+
    #> [1] 20
    # which of these are in the same study or studies as the first one?
+phenotype_matches(x, pk_get_study_list(phenotype = x$id[1]))
+
    #>  [1]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
+#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_class.html b/docs/reference/pk_class.html index 40e9da4..4b25157 100644 --- a/docs/reference/pk_class.html +++ b/docs/reference/pk_class.html @@ -8,21 +8,29 @@ Get term classification — pk_class • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,17 +117,15 @@

    Get term classification

    -

    Return direct superclasses, direct subclasses, and equivalent classes of a given term

    -
    - 
    pk_taxon_class(x, verbose = TRUE)
+    
    pk_taxon_class(x, verbose = TRUE)
 
-pk_anatomical_class(x, verbose = TRUE)
+pk_anatomical_class(x, verbose = TRUE)
+
+pk_phenotype_class(x, verbose = TRUE)
    
 
-pk_phenotype_class(x, verbose = TRUE)
    -

    Arguments

    @@ -131,37 +138,36 @@

    Arg

    logical: optional. If TRUE (default), informative messages printed.
    - +

    Value

    A list containing data.frame

    - - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_get_iri.html b/docs/reference/pk_get_iri.html index ace6def..1661202 100644 --- a/docs/reference/pk_get_iri.html +++ b/docs/reference/pk_get_iri.html @@ -8,21 +8,29 @@ Resolve a text query to IRI — pk_get_iri • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -72,7 +81,7 @@ -
    +
    @@ -109,15 +118,13 @@

    Resolve a text query to IRI

    -

    Finds the term matching the query text, and returns its IRI. If the query text is already a IRI, it is returned as is.

    -
    - 
    pk_get_iri(text, as, exactOnly = FALSE, nomatch = NA,
-  verbose = FALSE)
    - + 
    pk_get_iri(text, as, exactOnly = FALSE, nomatch = NA,
+  verbose = FALSE)
    +

    Arguments

    @@ -149,46 +156,42 @@

    Arg time-consuming operations. Default is FALSE.

    - +

    Value

    The IRI if a match is found.

    -

    Details

    This uses find_term to find matches, and assumes that the term of interest is a class. If there is an exact match, its IRI will be returned. If there isn't, by default partial, and as a last resort broad, matches will also be considered, although this will result in a warning.

    - - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_get_ontotrace_xml.html b/docs/reference/pk_get_ontotrace_xml.html index 9967489..298c768 100644 --- a/docs/reference/pk_get_ontotrace_xml.html +++ b/docs/reference/pk_get_ontotrace_xml.html @@ -8,21 +8,29 @@ Obtain a synthetic presence/absence matrix — pk_get_ontotrace_xml • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -73,7 +82,7 @@ -
    +
    @@ -110,16 +119,14 @@

    Obtain a synthetic presence/absence matrix

    -

    Queries the Phenoscape KB for a synthetic presence/absence character matrix for the given taxa and anatomical entities, and returns the result as a nexml object (from the RNeXML package).

    -
    - 
    pk_get_ontotrace_xml(taxon, entity, relation = "part of",
-  variable_only = TRUE, strict = TRUE)
    - + 
    pk_get_ontotrace_xml(taxon, entity, relation = "part of",
+  variable_only = TRUE, strict = TRUE)
    +

    Arguments

    @@ -155,11 +162,10 @@

    Arg result in an error.

    - +

    Value

    RNeXML::nexml object

    -

    Details

    The character matrix includes both asserted and logically inferred states. The @@ -167,64 +173,60 @@

    Details also includes all parts of the entities. See parameter relation for changing this. By default, only characters that are variable across the resulting taxa are included; use variable_only to change this.

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # one taxon (including subclasses), one entity (including subclasses and 
 # by default its parts)
-nex <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "fin")
+nex <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "fin")
 
 # same as above, except do not include parts or other relationships (fin
 # presence/absence does not vary across Ictalurus, hence need to allow
 # non-variable characters)
-nex <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "fin",
-                            relation = NA, variable_only = FALSE)
+nex <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "fin",
+                            relation = NA, variable_only = FALSE)
 
 # instead of parts, include entities in develops_from relationship to the query entity
-nex <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "paired fin bud",
-                            relation = "develops from", variable_only = FALSE)
+nex <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "paired fin bud",
+                            relation = "develops from", variable_only = FALSE)
 
 # query with multiple taxa, and/or multiple entities:
-nex <- pk_get_ontotrace_xml(taxon = c("Ictalurus", "Ameiurus"),
-                            entity = c("pectoral fin", "pelvic fin"))
+nex <- pk_get_ontotrace_xml(taxon = c("Ictalurus", "Ameiurus"),
+                            entity = c("pectoral fin", "pelvic fin"))
 
 # Use the RNeXML API to obtain the character matrix etc:
-m <- RNeXML::get_characters(nex)
-dim(m)      # number of taxa and characters
-rownames(m) # taxon names
-colnames(m) # characters (entity names)
+m <- RNeXML::get_characters(nex)
+dim(m)      # number of taxa and characters
+rownames(m) # taxon names
+colnames(m) # characters (entity names)
 
-# }
    
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_get_study.html b/docs/reference/pk_get_study.html index 661ce1b..a0e28e6 100644 --- a/docs/reference/pk_get_study.html +++ b/docs/reference/pk_get_study.html @@ -8,21 +8,29 @@ pk_get_study — pk_get_study • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,13 +117,11 @@

    pk_get_study

    -

    pk_get_study

    -
    - 
    pk_get_study(nexmls)
    - + 
    pk_get_study(nexmls)
    +

    Arguments

    @@ -123,46 +130,44 @@

    Arg

    a list of nexml objects
    - +

    Value

    A list of data.frames containing matrices

    -

    Examples

    - 
    # NOT RUN {
-slist <- pk_get_study_list(taxon = "Ameiurus", entity = "pelvic splint")
-nex_list <- pk_get_study_xml(slist$id) # get the list of NeXML objects for the studies
-pk_get_study(nex_list) # retrieve the study matrices
-pk_get_study_meta(nex_list) # retrieve the meta data for the studies
-# }
    + 
    if (FALSE) {
+slist <- pk_get_study_list(taxon = "Ameiurus", entity = "pelvic splint")
+nex_list <- pk_get_study_xml(slist$id) # get the list of NeXML objects for the studies
+pk_get_study(nex_list) # retrieve the study matrices
+pk_get_study_meta(nex_list) # retrieve the meta data for the studies
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_get_study_list.html b/docs/reference/pk_get_study_list.html index 08689b1..0d84b34 100644 --- a/docs/reference/pk_get_study_list.html +++ b/docs/reference/pk_get_study_list.html @@ -8,21 +8,29 @@ Query the list of studies by taxa, anatomical entities, and qualities. — pk_get_study_list • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -73,7 +82,7 @@ -
    +
    @@ -110,16 +119,14 @@

    Query the list of studies by taxa, anatomical entities, and qualities.

    -

    Return studies that contain taxa which are members of the optional input taxon, and characters which have phenotype annotations subsumed by the given entity and quality terms.

    -
    - 
    pk_get_study_list(taxon = NA, entity = NA, quality = NA,
-  phenotype = NA, includeRels = NA, relation = "part of")
    - + 
    pk_get_study_list(taxon = NA, entity = NA, quality = NA,
+  phenotype = NA, includeRels = NA, relation = "part of")
    +

    Arguments

    @@ -157,73 +164,71 @@

    Arg part of. Only used if includeRels is left at its default value.

    - +

    Value

    data.frame

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # by default, parts are included
-slist <- pk_get_study_list(taxon = "Siluridae", entity = "fin")
-colnames(slist)
-nrow(slist)
+slist <- pk_get_study_list(taxon = "Siluridae", entity = "fin")
+colnames(slist)
+nrow(slist)
 
 # can also disable parts
-slist <- pk_get_study_list(taxon = "Siluridae", entity = "fin", includeRels = FALSE)
-nrow(slist)
+slist <- pk_get_study_list(taxon = "Siluridae", entity = "fin", includeRels = FALSE)
+nrow(slist)
 
 # or filter studies only by entity, including their parts
-slist <- pk_get_study_list(entity = "pelvic fin", includeRels = c("part of"))
-nrow(slist)
+slist <- pk_get_study_list(entity = "pelvic fin", includeRels = c("part of"))
+nrow(slist)
 
 # or filter studies only by entity, including their parts
-slist <- pk_get_study_list(entity = "pelvic fin", includeRels = c("part of"))
-nrow(slist)
+slist <- pk_get_study_list(entity = "pelvic fin", includeRels = c("part of"))
+nrow(slist)
 
 # including not only parts but also historical and serial homologs
-slist <- pk_get_study_list(entity = "pelvic fin",
-                           includeRels = c("part of",
+slist <- pk_get_study_list(entity = "pelvic fin",
+                           includeRels = c("part of",
                                            "serially homologous to",
-                                           "historical homologous to"))
-nrow(slist)
+                                           "historical homologous to"))
+nrow(slist)
 # relationship names can be given as prefixes
-slist1 <- pk_get_study_list(entity = "pelvic fin",
-                            includeRels = c("part", "serial", "historical"))
-nrow(slist1) == nrow(slist)
+slist1 <- pk_get_study_list(entity = "pelvic fin",
+                            includeRels = c("part", "serial", "historical"))
+nrow(slist1) == nrow(slist)
 
 # or apply no filter, obtaining all studies in the KB
-slist <- pk_get_study_list()
-nrow(slist)
-# }
    
+slist <- pk_get_study_list()
+nrow(slist)
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_get_study_meta.html b/docs/reference/pk_get_study_meta.html index 14d90a9..ee36352 100644 --- a/docs/reference/pk_get_study_meta.html +++ b/docs/reference/pk_get_study_meta.html @@ -8,21 +8,29 @@ pk_get_study_meta — pk_get_study_meta • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,13 +117,11 @@

    pk_get_study_meta

    -

    pk_get_study_meta

    -
    - 
    pk_get_study_meta(nexmls)
    - + 
    pk_get_study_meta(nexmls)
    +

    Arguments

    @@ -123,46 +130,44 @@

    Arg

    a list of NeXML objects
    - +

    Value

    A list of data.frames containing taxa and characters

    -

    Examples

    - 
    # NOT RUN {
-slist <- pk_get_study_list(taxon = "Ameiurus", entity = "pelvic splint")
-nex_list <- pk_get_study_xml(slist$id) # get the list of NeXML objects for the studies
-pk_get_study(nex_list) # retrieve the study matrices
-pk_get_study_meta(nex_list) # retrieve the meta data for the studies
-# }
    + 
    if (FALSE) {
+slist <- pk_get_study_list(taxon = "Ameiurus", entity = "pelvic splint")
+nex_list <- pk_get_study_xml(slist$id) # get the list of NeXML objects for the studies
+pk_get_study(nex_list) # retrieve the study matrices
+pk_get_study_meta(nex_list) # retrieve the meta data for the studies
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_get_study_xml.html b/docs/reference/pk_get_study_xml.html index ea407cb..1302284 100644 --- a/docs/reference/pk_get_study_xml.html +++ b/docs/reference/pk_get_study_xml.html @@ -8,21 +8,29 @@ pk_get_study_xml — pk_get_study_xml • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,13 +117,11 @@

    pk_get_study_xml

    -

    pk_get_study_xml

    -
    - 
    pk_get_study_xml(study_ids)
    - + 
    pk_get_study_xml(study_ids)
    +

    Arguments

    @@ -123,44 +130,42 @@

    Arg

    a list of study IDs.
    - +

    Value

    A list of nexml objects

    -

    Examples

    - 
    # NOT RUN {
-slist <- pk_get_study_list(taxon = "Ameiurus", entity = "pelvic splint")
-nex_list <- pk_get_study_xml(slist$id)
-# }
    + 
    if (FALSE) {
+slist <- pk_get_study_list(taxon = "Ameiurus", entity = "pelvic splint")
+nex_list <- pk_get_study_xml(slist$id)
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_is_descendant.html b/docs/reference/pk_is_descendant.html index 5406fd2..761bc60 100644 --- a/docs/reference/pk_is_descendant.html +++ b/docs/reference/pk_is_descendant.html @@ -8,21 +8,29 @@ Test which candidate terms are ancestors or descendants of a term — pk_is_descendant • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -73,7 +82,7 @@ -
    +
    @@ -110,17 +119,15 @@

    Test which candidate terms are ancestors or descendants of a term

    -

    Tests which in a list of candidate terms are ancestors to or descendants of the query term. Note that terms are not considered ancestors and descendants of themselves.

    -
    - 
    pk_is_descendant(term, candidates, includeRels = c("none", "part_of"))
+    
    pk_is_descendant(term, candidates, includeRels = c("none", "part_of"))
+
+pk_is_ancestor(term, candidates, includeRels = c("none", "part_of"))
    
 
-pk_is_ancestor(term, candidates, includeRels = c("none", "part_of"))
    -

    Arguments

    @@ -141,12 +148,11 @@

    Arg sense for anatomy terms. The default is not to include these.

    - +

    Value

    A logical vector indicating which candidate terms are ancestors and descendants, respectively, of the query term.

    -

    Details

    Any of both the query term and the list of candidate terms can be supplied @@ -154,56 +160,52 @@

    Details to IRIs, allowing any ontology as the target. If labels aren't unique enough across ontologies, it is advisable to do the resolution before calling these functions, using pk_get_iri with the appropriate ontology set.

    -

    Examples

    - 
    # NOT RUN {
+    
    if (FALSE) {
 # taxa:
-pk_is_descendant("Halecostomi", c("Halecostomi", "Icteria", "Sciaenidae"))
-pk_is_ancestor("Sciaenidae", c("Halecostomi", "Abeomelomys", "Sciaenidae"))
+pk_is_descendant("Halecostomi", c("Halecostomi", "Icteria", "Sciaenidae"))
+pk_is_ancestor("Sciaenidae", c("Halecostomi", "Abeomelomys", "Sciaenidae"))
 
 # anatomical entities:
-pk_is_descendant("paired fin", c("pectoral fin", "pelvic fin", "dorsal fin"))
-pk_is_descendant("paired fin", c("pelvic fin", "pelvic fin ray"))
-pk_is_descendant("paired fin", c("pelvic fin", "pelvic fin ray"), includeRels = "part_of")
+pk_is_descendant("paired fin", c("pectoral fin", "pelvic fin", "dorsal fin"))
+pk_is_descendant("paired fin", c("pelvic fin", "pelvic fin ray"))
+pk_is_descendant("paired fin", c("pelvic fin", "pelvic fin ray"), includeRels = "part_of")
 
-pk_is_ancestor("pelvic fin", c("paired fin", "hindlimb", "fin"))
-pk_is_ancestor("pelvic fin ray", c("paired fin", "fin"))
-pk_is_ancestor("pelvic fin ray", c("paired fin", "fin"), includeRels = "part_of")
+pk_is_ancestor("pelvic fin", c("paired fin", "hindlimb", "fin"))
+pk_is_ancestor("pelvic fin ray", c("paired fin", "fin"))
+pk_is_ancestor("pelvic fin ray", c("paired fin", "fin"), includeRels = "part_of")
 
 # phenotypic quality
-pk_is_ancestor("triangular", c("shape", "color", "amount"))
-pk_is_descendant("shape", c("T-shaped", "star shaped", "yellow"))
-# }
    
+pk_is_ancestor("triangular", c("shape", "color", "amount"))
+pk_is_descendant("shape", c("T-shaped", "star shaped", "yellow"))
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_is_extinct.html b/docs/reference/pk_is_extinct.html index 4807732..79db436 100644 --- a/docs/reference/pk_is_extinct.html +++ b/docs/reference/pk_is_extinct.html @@ -8,21 +8,29 @@ Determine which taxa are extinct — pk_is_extinct • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +38,10 @@ - + - + @@ -47,9 +55,10 @@ + - +
    @@ -71,7 +80,7 @@ -
    +
    @@ -108,13 +117,11 @@

    Determine which taxa are extinct

    -

    This is simply a convenience function on top of pk_taxon_detail().

    -
    - 
    pk_is_extinct(taxon, verbose = FALSE)
    - + 
    pk_is_extinct(taxon, verbose = FALSE)
    +

    Arguments

    @@ -130,40 +137,39 @@

    Arg possibly time-consuming operations. The default is FALSE.

    - +

    Value

    A logical named vector with value TRUE if the corresponding input taxon is marked as extinct, and FALSE otherwise. For taxon names that failed to be looked up, the value will be NA. Names will be the input taxa where there were given as names, and the label of the respective taxon otherwise.

    - - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_ontotrace.html b/docs/reference/pk_ontotrace.html index 2e2098b..cae7fb6 100644 --- a/docs/reference/pk_ontotrace.html +++ b/docs/reference/pk_ontotrace.html @@ -8,21 +8,29 @@ Returns a NeXML-format evolutionary character matrix. — pk_ontotrace • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +38,12 @@ - + - + @@ -49,9 +57,10 @@ + - +
    @@ -73,7 +82,7 @@ -
    +
    @@ -110,17 +119,15 @@

    Returns a NeXML-format evolutionary character matrix.

    -

    Generate matrix of inferred presence/absence associations for anatomical structures subsumed by the provided entity class expression, for any taxa within the provided taxon class expression.

    -
    - 
    pk_get_ontotrace(nex)
+    
    pk_get_ontotrace(nex)
+
+pk_get_ontotrace_meta(nex)
    
 
-pk_get_ontotrace_meta(nex)
    -

    Arguments

    @@ -129,47 +136,45 @@

    Arg

    a nexml object
    - +

    Value

    data.frame: The OntoTrace matrix.

    -

    Examples

    - 
    # NOT RUN {
-nex0 <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "fin")
-
-nex <- pk_get_ontotrace_xml(taxon = c("Ictalurus", "Ameiurus"), entity = "fin spine")
-pk_get_ontotrace(nex)
-pk_get_ontotrace_meta(nex)
-# }
    + 
    if (FALSE) {
+nex0 <- pk_get_ontotrace_xml(taxon = "Ictalurus", entity = "fin")
+
+nex <- pk_get_ontotrace_xml(taxon = c("Ictalurus", "Ameiurus"), entity = "fin spine")
+pk_get_ontotrace(nex)
+pk_get_ontotrace_meta(nex)
+}
+
    - +
    -

    Developed by Hong Xu, Hilmar Lapp.

    +

    Developed by Hong Xu, Hilmar Lapp, John Bradley.

    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.6.1.

    +
    + + diff --git a/docs/reference/pk_terms.html b/docs/reference/pk_terms.html index 92120a6..17a2604 100644 --- a/docs/reference/pk_terms.html +++ b/docs/reference/pk_terms.html @@ -8,21 +8,29 @@ Get term details (ID, label, definition) — pk_terms • rphenoscape + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ + - +
    @@ -72,7 +81,7 @@ -
    +
    @@ -109,20 +118,18 @@

    Get term details (ID, label, definition)

    -

    Retrieve details about a taxon, an anatomical structure, a gene, or a phenotypic quality.

    -
    - 
    pk_taxon_detail(term, verbose = FALSE)
+    
    pk_taxon_detail(term, verbose = FALSE)
 
-pk_anatomical_detail(term, verbose = FALSE)
+pk_anatomical_detail(term, verbose = FALSE)
 
-pk_phenotype_detail(term, verbose = FALSE)
+pk_phenotype_detail(term, verbose = FALSE)
+
+pk_gene_detail(term, taxon = NA, verbose = FALSE)
    
 
-pk_gene_detail(term, taxon = NA, verbose = FALSE)
    -

    Arguments

    @@ -144,7 +151,7 @@

    Arg ontology IRI for which to match the gene name.

    - +

    Value

    A data.frame, with at least columns "id" and "label".

    @@ -156,18 +163,20 @@

    Value

    For pk_gene_detail, the additional columns are "taxon.id" and "taxon.label" for the corresponding NCBI Taxonomy ID and name, and "matchType" ('exact' or 'partial').

    -

    Examples

    - 
    pk_taxon_detail("Coralliozetus")
    #>                                           id         label extinct
+    
    pk_taxon_detail("Coralliozetus")
+
    #>                                           id         label extinct
 #> 1 http://purl.obolibrary.org/obo/VTO_0042955 Coralliozetus   FALSE
 #>                                          rank.id rank.label common_name
-#> 1 http://purl.obolibrary.org/obo/TAXRANK_0000005      genus        <NA>
    pk_anatomical_detail("basihyal bone")
    #>           label
-#> 1 basihyal bone
+#> 1 http://purl.obolibrary.org/obo/TAXRANK_0000005      genus        <NA>
    pk_anatomical_detail("basihyal bone")
+
    #>           label                               isDefinedBy
+#> 1 basihyal bone http://purl.obolibrary.org/obo/uberon.owl
 #>                                                                                 definition
 #> 1 Replacement bone that is median and is the anterior-most bone of the ventral hyoid arch.
 #>                                              id
-#> 1 http://purl.obolibrary.org/obo/UBERON_0011618
    pk_gene_detail("socs5")
    #>                                                  id  label matchType
+#> 1 http://purl.obolibrary.org/obo/UBERON_0011618
    pk_gene_detail("socs5")
+
    #>                                                  id  label matchType
 #> 1             http://xenbase.org/XB-GENEPAGE-479592  socs5     exact
 #> 2 http://www.informatics.jax.org/marker/MGI:2385459  Socs5     exact
 #> 3               http://zfin.org/ZDB-GENE-061013-408 socs5a   partial
@@ -179,32 +188,30 @@ 
    Examp
 #> 4  http://purl.obolibrary.org/obo/NCBITaxon_7955  Danio rerio
    
 
    
   
    
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
+
       
    
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/pkb_args_to_query.html b/docs/reference/pkb_args_to_query.html
index 7f8baf9..d72c707 100644
--- a/docs/reference/pkb_args_to_query.html
+++ b/docs/reference/pkb_args_to_query.html
@@ -8,21 +8,29 @@
 
 Creates a list of named query parameters — pkb_args_to_query • rphenoscape
 
+
 
-
+
 
 
-
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+
+
+
+
+
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+
 
 
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+
 
 
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+
 
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+
 
 
 
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+
 
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+
 
 
 
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+
   
 
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-      
       
    
 
       
+
       
 
 
    
@@ -111,16 +120,14 @@ 
    Creates a list of named query parameters
    
     
    
 
     
    
-    
     
    Several Phenoscape KB API endpoints use a form-like parameter list for
 filtering (limiting), or, in the case of relationships, expanding, the
 query result. This function aids in preparing the query string for these
 endpoints. It is internal to the package.
    
-    
     
    
 
-    
    pkb_args_to_query(..., includeRels = FALSE, verbose = FALSE)
    
-    
+    
    pkb_args_to_query(..., includeRels = FALSE, verbose = FALSE)
    
+
     
    Arguments
    
     
@@ -146,38 +153,37 @@ 
    Arg
 operations are run.
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    A list of named query parameters suitatoble for several form-like
 query endpoints in the Phenoscape KB API.
    
-    
 
   
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
+
       
    
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/profile_similarity.html b/docs/reference/profile_similarity.html
index 80a3e35..3b9e6d4 100644
--- a/docs/reference/profile_similarity.html
+++ b/docs/reference/profile_similarity.html
@@ -8,21 +8,29 @@
 
 Semantic similarity between profiles — profile_similarity • rphenoscape
 
+
 
-
+
 
 
-
-
+
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+
+
+
+
+
 
 
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+
+
 
 
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+
 
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+
 
 
 
@@ -30,8 +38,8 @@
 
 
 
-
 
+
 
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+
 
 
 
@@ -58,9 +66,10 @@
 
 
 
+
   
 
-  
+  
     
    
       
    
       
 
@@ -82,7 +91,7 @@
       
-      
       
    
 
       
+
       
 
 
    
@@ -119,7 +128,6 @@ 
    Semantic similarity between profiles
    
     
    
 
     
    
-    
     
    Calculates the semantic similarity between profiles (groups) of terms.
    
 
    bestPairs aggregates pairwise scores by "best pairs" between two profiles.
 That is, for profiles P1 and P2 with terms T1[i] (i = 1,...n) and T2[j]
@@ -132,15 +140,14 @@ 
    Semantic similarity between profiles
    
 similarity scores such that the diagonal of the pair-wise similarity matrix
 is ignored. This may be desirable, for example, when average with-in group
 similarity should exclude the similarity of terms to themselves.
    
-    
     
    
 
-    
    profile_similarity(pairwise, subsumer_mat, ..., f, reduce = NA)
+    
    profile_similarity(pairwise, subsumer_mat, ..., f, reduce = NA)
+
+bestPairs(X, best = max, aggregate = mean)
 
-bestPairs(X, best = max, aggregate = mean)
+reduce.ignoringDiag(X, aggregate = mean)
    
 
-reduce.ignoringDiag(X, aggregate = mean)
    
-    
     
    Arguments
    
     
@@ -163,7 +170,7 @@ 
    Arg
     
     
    
-      
@@ -185,17 +192,17 @@ 
    Arg
     
    
-      
+      
+NA values before calculating the aggregate. The default is mean().
    
     
    
       f
    a factor (or an object coercible to factor) defining the group
+      
    a factor (or an object coercible to factor) defining the group
 (profile) membership of the terms (= columns) in the subsumer matrix.
 Columns and rows of the resulting profile similarity matrix will take their
 names from the levels of the factor. The factor may have 2 or more levels.
    
     
    
       best
    the function for determing the best score. The default is max().
    the function for determing the best score. The default is max().
    		
     
    
     
    
       aggregate
       
    the function for aggregating scores (for reduce.ignoringDiag)
 or best pairwise scores (for bestPairs). For reduce.ignoringDiag, the
 function must also accept parameter na.rm, and if the value is TRUE, remove
-NA values before calculating the aggregate. The default is mean().
    		
     
    
     
    
-    
+
     
    Details
    
 
     
    A profile refers to a group of terms, and profile similarity to the similarity
@@ -209,7 +216,7 @@ 
    Details
 and then the pairwise scores between the terms in two groups are reduced
 to a single score giving the between-group score.
    
 
-    
+
     
    Note
    
 
     
    In pairwise mode, if the reduce function is asymmetric (as will typically be
@@ -217,85 +224,88 @@ 
    Note
    
 of the profile similarity matrix will not be symmetric. If a symmetric similarity
 matrix is desired, this can be achieved by computing (X +  t(X)) / 2, if X is
 the profile similarity matrix.
    
-    
 
     
    Examples
    
-    
    tt <- sapply(c("pelvic fin", "pectoral fin",
-               "forelimb", "hindlimb", "dorsal fin", "caudal fin"),
-             pk_get_iri, as = "anatomy")
+    
    tt <- sapply(c("pelvic fin", "pectoral fin",
+               "forelimb", "hindlimb", "dorsal fin", "caudal fin"),
+             pk_get_iri, as = "anatomy")
 
 # define groups (profiles) as factors:
-pairedUnpaired <- c(rep("paired", times = 4), rep("unpaired", times = 2))
-finsLimbs <- c("fins", "fins", "limbs", "limbs", "fins", "fins")
-pairedFinLimb <- interaction(as.factor(pairedUnpaired), as.factor(finsLimbs))
+pairedUnpaired <- c(rep("paired", times = 4), rep("unpaired", times = 2))
+finsLimbs <- c("fins", "fins", "limbs", "limbs", "fins", "fins")
+pairedFinLimb <- interaction(as.factor(pairedUnpaired), as.factor(finsLimbs))
 
 # compute subsumer matrix
-subs.mat <- subsumer_matrix(tt, .colnames = "label", .labels = names(tt),
-                            preserveOrder = TRUE)
+subs.mat <- subsumer_matrix(tt, .colnames = "label", .labels = names(tt),
+                            preserveOrder = TRUE)
 # group-wise profile similarity:
-profile_similarity(jaccard_similarity, subs.mat, f = pairedUnpaired)
    #>             paired  unpaired
-#> paired   1.0000000 0.3163265
-#> unpaired 0.3163265 1.0000000
    profile_similarity(jaccard_similarity, subs.mat, f = finsLimbs)
    #>            fins     limbs
-#> fins  1.0000000 0.7653061
-#> limbs 0.7653061 1.0000000
    profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb)
    #>               paired.fins unpaired.fins paired.limbs
-#> paired.fins     1.0000000     0.3483146    0.8152174
-#> unpaired.fins   0.3483146     1.0000000    0.3152174
-#> paired.limbs    0.8152174     0.3152174    1.0000000
    
+profile_similarity(jaccard_similarity, subs.mat, f = pairedUnpaired)
+
    #>             paired  unpaired
+#> paired   1.0000000 0.3366337
+#> unpaired 0.3366337 1.0000000
    profile_similarity(jaccard_similarity, subs.mat, f = finsLimbs)
+
    #>            fins     limbs
+#> fins  1.0000000 0.7722772
+#> limbs 0.7722772 1.0000000
    profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb)
+
    #>               paired.fins unpaired.fins paired.limbs
+#> paired.fins     1.0000000     0.3695652    0.8210526
+#> unpaired.fins   0.3695652     1.0000000    0.3368421
+#> paired.limbs    0.8210526     0.3368421    1.0000000
    
 # pairwise, using mean (average pairwise score); result is symmetric
-profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
-                   reduce = mean)
    #>               paired.fins unpaired.fins paired.limbs
-#> paired.fins     0.9397590     0.3742470    0.8251232
-#> unpaired.fins   0.3742470     0.9189189    0.3413199
-#> paired.limbs    0.8251232     0.3413199    0.9285714
    # the same, but excluding self-similarity of terms within groups
-profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
-                   reduce = reduce.ignoringDiag)
    #>               paired.fins unpaired.fins paired.limbs
-#> paired.fins     0.8795181     0.3742470    0.8251232
-#> unpaired.fins   0.3742470     0.8378378    0.3413199
-#> paired.limbs    0.8251232     0.3413199    0.8571429
    # pairwise, using max; result is symmetric
-profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
-                   reduce = max)
    #>               paired.fins unpaired.fins paired.limbs
-#> paired.fins     1.0000000     0.3750000    0.8571429
-#> unpaired.fins   0.3750000     1.0000000    0.3414634
-#> paired.limbs    0.8571429     0.3414634    1.0000000
    # pairwise, using average of best pairs; result is _not_ symmetric
-sm <- profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
-                         reduce = bestPairs)
-sm
    #>               paired.fins unpaired.fins paired.limbs
-#> paired.fins     1.0000000     0.3750000    0.8571429
-#> unpaired.fins   0.3742470     1.0000000    0.3413199
-#> paired.limbs    0.8571429     0.3414634    1.0000000
    # make symmtric, for example by averaging:
-(sm + t(sm)) / 2
    #>               paired.fins unpaired.fins paired.limbs
-#> paired.fins     1.0000000     0.3746235    0.8571429
-#> unpaired.fins   0.3746235     1.0000000    0.3413917
-#> paired.limbs    0.8571429     0.3413917    1.0000000
    
+profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
+                   reduce = mean)
+
    #>               paired.fins unpaired.fins paired.limbs
+#> paired.fins     0.9418605     0.3964696    0.8310345
+#> unpaired.fins   0.3964696     0.9250000    0.3641711
+#> paired.limbs    0.8310345     0.3641711    0.9310345
    # the same, but excluding self-similarity of terms within groups
+profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
+                   reduce = reduce.ignoringDiag)
+
    #>               paired.fins unpaired.fins paired.limbs
+#> paired.fins     0.8837209     0.3964696    0.8310345
+#> unpaired.fins   0.3964696     0.8500000    0.3641711
+#> paired.limbs    0.8310345     0.3641711    0.8620690
    # pairwise, using max; result is symmetric
+profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
+                   reduce = max)
+
    #>               paired.fins unpaired.fins paired.limbs
+#> paired.fins     1.0000000     0.3975904    0.8620690
+#> unpaired.fins   0.3975904     1.0000000    0.3647059
+#> paired.limbs    0.8620690     0.3647059    1.0000000
    # pairwise, using average of best pairs; result is _not_ symmetric
+sm <- profile_similarity(jaccard_similarity, subs.mat, f = pairedFinLimb,
+                         reduce = bestPairs)
+sm
+
    #>               paired.fins unpaired.fins paired.limbs
+#> paired.fins     1.0000000     0.3975904    0.8620690
+#> unpaired.fins   0.3964696     1.0000000    0.3641711
+#> paired.limbs    0.8620690     0.3647059    1.0000000
    # make symmtric, for example by averaging:
+(sm + t(sm)) / 2
+
    #>               paired.fins unpaired.fins paired.limbs
+#> paired.fins      1.000000     0.3970300    0.8620690
+#> unpaired.fins    0.397030     1.0000000    0.3644385
+#> paired.limbs     0.862069     0.3644385    1.0000000
    
   
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
+
       
    
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/similarity.html b/docs/reference/similarity.html
index 732b850..6ddaa4b 100644
--- a/docs/reference/similarity.html
+++ b/docs/reference/similarity.html
@@ -8,21 +8,29 @@
 
 Compute semantic similarity metrics between terms — similarity • rphenoscape
 
+
 
-
+
 
 
-
-
+
+
+
+
+
+
+
 
 
-
+
+
 
 
-
+
 
-
-
+
+
+
 
 
 
@@ -30,8 +38,8 @@
 
 
 
-
 
+
 
-
+
 
 
 
@@ -67,9 +75,10 @@
 
 
 
+
   
 
-  
+  
     
    
       
    
       
 
@@ -91,7 +100,7 @@
       
-      
       
    
 
       
+
       
 
 
    
@@ -128,7 +137,6 @@ 
    Compute semantic similarity metrics between terms
    
     
    
 
     
    
-    
     
    The Tanimoto similarity ST is computed according to the definition for bit vectors
 (see Jaccard index at Wikipedia).
 For weights \(W_i \in \{0, 1\}\) it is the same as the
@@ -150,18 +158,17 @@ 
    Compute semantic similarity metrics between terms
    
 
    The Resnik similarity between two terms is the information content (IC) of
 their most informative common ancestor (MICA), which is the common subsumer
 with the greatest information content.
    
-    
     
    
 
-    
    tanimoto_similarity(subsumer_mat = NA, terms = NULL, ...)
+    
    tanimoto_similarity(subsumer_mat = NA, terms = NULL, ...)
+
+jaccard_similarity(subsumer_mat = NA, terms = NULL, ...)
 
-jaccard_similarity(subsumer_mat = NA, terms = NULL, ...)
+cosine_similarity(subsumer_mat = NA, terms = NULL, ...)
 
-cosine_similarity(subsumer_mat = NA, terms = NULL, ...)
+resnik_similarity(subsumer_mat = NA, terms = NULL, ...,
+  wt = term_freqs, wt_args = list(), base = 10)
    
 
-resnik_similarity(subsumer_mat = NA, terms = NULL, ...,
-  wt = term_freqs, wt_args = list(), base = 10)
    
-    
     
    Arguments
    
     
@@ -191,7 +198,9 @@ 
    Arg
 information content, and where a term will always have a score equal to or
 greater than any of its superclasses. If a function, it must accept parameter
 x as the vector of term IRIs and return a vector of frequencies (not
-IC scores) for the terms. The default is to use function term_freqs().
    
+IC scores) for the terms. The default is to use function term_freqs().
+Subsumer terms with zero or missing (NA) frequency will be omitted from the
+calculation.
    
     
     
    
@@ -205,67 +214,63 @@ 
    Arg
 content from term frequency. The default is 10.
    
     
    
     
    
       wt_args
    
     
    
-    
+
     
    Value
    
 
     
    A matrix with M[i,j] = similarity of terms i and j.
    
-    
     
    References
    
 
     
    Philip Resnik (1995). "Using information content to evaluate semantic
 similarity in a taxonomy". Proceedings of the 14th International Joint
 Conference on Artificial Intelligence (IJCAI'95). 1: 448–453
    
-    
 
     
    Examples
    
-    
    # NOT RUN {
-sm <- jaccard_similarity(terms = c("pelvic fin", "pectoral fin",
+    
    if (FALSE) {
+sm <- jaccard_similarity(terms = c("pelvic fin", "pectoral fin",
                                    "forelimb", "hindlimb",
-                                   "dorsal fin", "caudal fin"),
-                         .colnames = "label")
-sm
+                                   "dorsal fin", "caudal fin"),
+                         .colnames = "label")
+sm
 
 # e.g., turn into distance matrix, cluster, and plot
-plot(hclust(as.dist(1-sm)))
-# }# NOT RUN {
-phens <- get_phenotypes("basihyal bone", taxon = "Cyprinidae")
-sm.ic <- resnik_similarity(terms = phens$id,
-                           .colnames = "label", .labels = phens$label,
-                           wt_args = list(as = "phenotype",
-                                          corpus = "taxa"))
-maxIC <- -log10(1 / corpus_size("taxa"))
+plot(hclust(as.dist(1-sm)))
+}
+if (FALSE) {
+phens <- get_phenotypes("basihyal bone", taxon = "Cyprinidae")
+sm.ic <- resnik_similarity(terms = phens$id,
+                           .colnames = "label", .labels = phens$label,
+                           wt_args = list(as = "phenotype",
+                                          corpus = "taxa"))
+maxIC <- -log10(1 / corpus_size("taxa"))
 # normalize by max IC, turn into distance matrix, cluster, and plot
-plot(hclust(as.dist(1-sm.ic/maxIC)))
-# }
    
+plot(hclust(as.dist(1-sm.ic/maxIC)))
+}
+
    
   
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
+
       
    
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/subsumer_matrix.html b/docs/reference/subsumer_matrix.html
index 7f22317..dac5820 100644
--- a/docs/reference/subsumer_matrix.html
+++ b/docs/reference/subsumer_matrix.html
@@ -8,21 +8,29 @@
 
 Obtains a subsumer matrix — subsumer_matrix • rphenoscape
 
+
 
-
+
 
 
-
-
+
+
+
+
+
+
+
 
 
-
+
+
 
 
-
+
 
-
-
+
+
+
 
 
 
@@ -30,12 +38,12 @@
 
 
 
-
 
+
 
-
+
 
 
 
@@ -49,9 +57,10 @@
 
 
 
+
   
 
-  
+  
     
    
       
    
       
 
@@ -73,7 +82,7 @@
       
-      
       
    
 
       
+
       
 
 
    
@@ -110,16 +119,14 @@ 
    Obtains a subsumer matrix
    
     
    
 
     
    
-    
     
    A subsumer matrix M for terms \(j \in \{1, \dots, n\}\)
 has value \(M_{i,j}=1\) iff class i (which can be an anonymous class expression) subsumes term j, and zero
 otherwise. Therefore, it will have n columns, one for each term.
    
-    
     
    
 
-    
    subsumer_matrix(terms, .colnames = c("ID", "IRI", "label"),
-  .labels = NULL, preserveOrder = FALSE, verbose = FALSE)
    
-    
+    
    subsumer_matrix(terms, .colnames = c("ID", "IRI", "label"),
+  .labels = NULL, preserveOrder = FALSE, verbose = FALSE)
    
+
     
    Arguments
    
     
@@ -160,7 +167,7 @@ 
    Arg
 potentially time-consuming operations.
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    A data.frame representing the subsumer matrix
    
@@ -171,7 +178,6 @@ 
    Value
    
 have attribute term.iris, giving the term IRIs for the rows (and columns).
 Note that these extra attributes will be lost upon subsetting the returned
 matrix.
    
-    
     
    Details
    
 
     
    In this implementation, for each row i
@@ -181,53 +187,49 @@ 
    Details
 very many) classes not subsuming any of the terms will not be included. This
 subsumer matrix is thus only useful for similarity metrics for which
 non-subsuming terms can be ignored.
    
-    
 
     
    Examples
    
-    
    # NOT RUN {
-tl <- c("http://purl.obolibrary.org/obo/UBERON_0000981",
+    
    if (FALSE) {
+tl <- c("http://purl.obolibrary.org/obo/UBERON_0000981",
         "http://purl.obolibrary.org/obo/UBERON_0002103",
         "http://purl.obolibrary.org/obo/UBERON_0000976",
-        "http://purl.obolibrary.org/obo/UBERON_0002102")
-m <- subsumer_matrix(tl)
-m <- # term IDs as column names
-id_prefixes <- attr(m, "prefixes")
-id_prefixes # 4x "http://purl.obolibrary.org/obo/"
-
-m <- subsumer_matrix(tl, .colnames = "label")
-m # term labels as column names
-mat_terms <- attr(m, "term.iris")
-mat_terms # term IRIs in the same order as columns
-# }
    
+        "http://purl.obolibrary.org/obo/UBERON_0002102")
+m <- subsumer_matrix(tl)
+m <- # term IDs as column names
+id_prefixes <- attr(m, "prefixes")
+id_prefixes # 4x "http://purl.obolibrary.org/obo/"
+
+m <- subsumer_matrix(tl, .colnames = "label")
+m # term labels as column names
+mat_terms <- attr(m, "term.iris")
+mat_terms # term IRIs in the same order as columns
+}
+
    
   
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
+
       
    
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/taxon_ontology_iris.html b/docs/reference/taxon_ontology_iris.html
index ab03cd3..e1bbc85 100644
--- a/docs/reference/taxon_ontology_iris.html
+++ b/docs/reference/taxon_ontology_iris.html
@@ -8,21 +8,29 @@
 
 Get IRIs of ontologies with taxonomy terms — taxon_ontology_iris • rphenoscape
 
+
 
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    Get IRIs of ontologies with taxonomy terms
    
     
    
 
     
    
-    
     
    Obtains the IRIs of taxon ontologies in the Phenoscape KB.
    
-    
     
    
 
-    
    taxon_ontology_iris()
    
-        
+    
    taxon_ontology_iris()
    
+
+
     
    Value
    
 
     
    A character vector
    
-    
 
   
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
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+
diff --git a/docs/reference/term_category.html b/docs/reference/term_category.html
index ea1ce66..a09d20b 100644
--- a/docs/reference/term_category.html
+++ b/docs/reference/term_category.html
@@ -8,21 +8,29 @@
 
 Determine the general category of terms — term_category • rphenoscape
 
+
 
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    Determine the general category of terms
    
     
    
 
     
    
-    
     
    Terms in the Phenoscape KB fall into different general categories: entity,
 quality, phenotype (which typically are entity-quality compositions), and
 taxon. The category is sometimes needed to plug a term IRI into the right
 parameter for a function or API call.
    
-    
     
    
 
-    
    term_category(x)
    
-    
+    
    term_category(x)
    
+
     
    Arguments
    
     
@@ -130,12 +137,11 @@ 
    Arg
 objects (such as phenotype objects)
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    A character vector with the term categories ("entity", "quality",
 "phenotype", or "taxon") of the terms in the input list.
    
-    
     
    Details
    
 
     
    The implementation will first try infer the category from the object type
@@ -143,43 +149,40 @@ 
    Details
 it will rely subsumption by specific upper ontology terms, specifically
 the BFO terms "independent continuant" (for entity terms) and "quality"
 (for quality terms).
    
-    
 
     
    Examples
    
-    
    term_category(c("http://purl.obolibrary.org/obo/UBERON_0011618",
+    
    term_category(c("http://purl.obolibrary.org/obo/UBERON_0011618",
                 "http://purl.obolibrary.org/obo/PATO_0002279",
                 "http://purl.obolibrary.org/obo/VTO_0071642",
-                "http://purl.obolibrary.org/obo/MP_0030825"))
    #> [1] "entity"    "quality"   "taxon"     "phenotype"
    phens <- get_phenotypes("basihyal bone")
-term_category(phens$id[1:3])
    #> [1] "phenotype" "phenotype" "phenotype"
    
+                "http://purl.obolibrary.org/obo/MP_0030825"))
+
    #> [1] "entity"    "quality"   "taxon"     "phenotype"
    phens <- get_phenotypes("basihyal bone")
+term_category(phens$id[1:3])
+
    #> [1] "phenotype" "phenotype" "phenotype"
    
   
-  
 
+
       
    
       
    
-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
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+  
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diff --git a/docs/reference/term_freqs.html b/docs/reference/term_freqs.html
index 7078433..541f944 100644
--- a/docs/reference/term_freqs.html
+++ b/docs/reference/term_freqs.html
@@ -8,21 +8,29 @@
 
 Obtains term frequencies for the Phenoscape KB — term_freqs • rphenoscape
 
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    Obtains term frequencies for the Phenoscape KB
    
     
    
 
     
    
-    
     
    Determines the frequencies for the given input list of terms, based on
 the selected corpus.
    
-    
     
    
 
-    
    term_freqs(x, as = c("auto", "entity", "quality", "phenotype"),
-  corpus = c("taxon_annotations", "taxa", "gene_annotations", "genes"),
-  decodeIRI = TRUE, ...)
    
-    
+    
    term_freqs(x, as = c("auto", "entity", "quality", "phenotype"),
+  corpus = c("taxon_annotations", "taxa", "gene_annotations", "genes"),
+  decodeIRI = TRUE, ...)
    
+
     
    Arguments
    
     
@@ -164,12 +171,11 @@ 
    Arg
 It can also be used to always include parts for entity terms.
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    a vector of frequencies as floating point numbers (between zero
 and 1.0), of the same length (and ordering) as the input list of terms.
    
-    
     
    Details
    
 
     
    Depending on the corpus selected, the frequencies are queried directly
@@ -183,7 +189,6 @@ 
    Details
 Phenoscape KB, resulting in counts of zero for such terms. For some of these
 the implementation here will try to rewrite the query (see parameter
 decodeIRI), but this only works to a limited extent.
    
-    
     
    Note
    
 
     
    Term categories being accurate is vital for obtaining correct counts and
@@ -198,52 +203,48 @@ 
    Note
    
 result as as. If all terms are of the same category and the category is
 known beforehand, it saves time and prevents potential errors to supply this
 category using as.
    
-    
 
     
    Examples
    
-    
    terms <- c("pectoral fin", "pelvic fin", "dorsal fin", "paired fin")
-IRIs <- sapply(terms, pk_get_iri, as = "anatomy")
-term_freqs(IRIs)
    #> [1] 0.001797967 0.002695709 0.004368265 0.004585561
    
-phens <- get_phenotypes(entity = "basihyal bone")
-term_freqs(phens$id, as = "phenotype", corpus = "taxon_annotations")
    #>  [1] 3.973408e-05 4.966760e-06 1.365859e-05 1.129938e-04 6.208450e-06
-#>  [6] 2.607549e-05 6.332619e-05 2.222625e-04 1.365859e-05 1.328608e-04
-#> [11] 4.966760e-06 6.518872e-04 8.940168e-05 2.619966e-04 5.090929e-05
-#> [16] 1.862535e-05 1.192022e-04 2.235042e-05 1.030603e-04
    term_freqs(phens$id, as = "phenotype", corpus = "taxa")
    #>  [1] 0.002659574          NA 0.002659574 0.002659574 0.001329787 0.001329787
-#>  [7] 0.002659574 0.001329787 0.002659574 0.005319149 0.002659574 0.005319149
-#> [13] 0.001329787 0.002659574 0.002659574          NA 0.003989362 0.001329787
-#> [19] 0.001329787
    
+    
    terms <- c("pectoral fin", "pelvic fin", "dorsal fin", "paired fin")
+IRIs <- sapply(terms, pk_get_iri, as = "anatomy")
+term_freqs(IRIs)
+
    #> [1] 0.001791597 0.002191650 0.004333911 0.004073383
    
+phens <- get_phenotypes(entity = "basihyal bone")
+term_freqs(phens$id, as = "phenotype", corpus = "taxon_annotations")
+
    #>  [1] 3.951144e-05 4.938930e-06 1.358206e-05 1.123607e-04 6.173663e-06
+#>  [6] 2.592938e-05 6.297136e-05 2.210171e-04 2.222519e-04 1.358206e-05
+#> [11] 1.358206e-04 4.938930e-06 6.494693e-04 8.890074e-05 2.617633e-04
+#> [16] 5.185877e-05 1.852099e-05 1.185343e-04 2.222519e-05 1.024828e-04
    term_freqs(phens$id, as = "phenotype", corpus = "taxa")
+
    #>  [1] 0.002547771 0.000000000 0.002547771 0.002547771 0.001273885 0.001273885
+#>  [7] 0.002547771 0.001273885 0.001273885 0.002547771 0.005095541 0.002547771
+#> [13] 0.005095541 0.001273885 0.002547771 0.002547771 0.000000000 0.003821656
+#> [19] 0.001273885 0.001273885
    
 
    
   
    
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-  
    Developed by Hong Xu, Hilmar Lapp.
    
+  
    Developed by Hong Xu, Hilmar Lapp, John Bradley.
    
 
    
 
 
    
-  
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+  
    Site built with pkgdown 1.6.1.
    
 
    
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diff --git a/docs/reference/term_iri.html b/docs/reference/term_iri.html
index 5bccdb2..7451ff5 100644
--- a/docs/reference/term_iri.html
+++ b/docs/reference/term_iri.html
@@ -8,21 +8,29 @@
 
 Obtain IRI(s) for canonical terms and properties — partOf_iri • rphenoscape
 
+
 
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    Obtain IRI(s) for canonical terms and properties
    
     
    
 
     
    
-    
     
    partOf_iri returns the IRI ofthe canonical "part_of" relationship in the
 database.
    
 
    hasPart_iri returns the IRI ofthe canonical "has_part" relationship in the
 database.
    
 
    Provides cached access to IRIs of terms and properties that are frequently used.
    
-    
     
    
 
-    
    partOf_iri()
+    
    partOf_iri()
+
+hasPart_iri()
 
-hasPart_iri()
+term_iri(label, type = "owl:Class", preferOntologies = NULL,
+  firstOnly = TRUE)
    
 
-term_iri(label, type = "owl:Class", preferOntologies = NULL,
-  firstOnly = TRUE)
    
-    
     
    Arguments
    
     
@@ -157,11 +164,10 @@ 
    Arg
 multiple matches. The default is TRUE.
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    Character, the IRI(s) for the requested term or property.
    
-    
     
    Details
    
 
     
    Requested IRIs are not hard-coded. Instead, they are dynamically retrieved from
@@ -171,40 +177,38 @@ 
    Details
 
    For the frequently needed properties "part of", "has part" etc, one should use
 the predefined functions (partOf_iri(), hasPart_iri()), so that the correct
 matches are cached and used internally by the package.
    
-    
 
     
    Examples
    
-    
    term_iri("part of", type = "owl:ObjectProperty", preferOntologies = c("RO", "BFO"))
    #> [1] "http://purl.obolibrary.org/obo/BFO_0000050"
    term_iri("develops from", type = "owl:ObjectProperty", preferOntologies = c("RO"))
    #> [1] "http://purl.obolibrary.org/obo/RO_0002202"
    term_iri("anatomical structure", firstOnly = FALSE)
    #> [1] "http://purl.obolibrary.org/obo/UBERON_0000061"
+    
    term_iri("part of", type = "owl:ObjectProperty", preferOntologies = c("RO", "BFO"))
+
    #> [1] "http://purl.obolibrary.org/obo/BFO_0000050"
    term_iri("develops from", type = "owl:ObjectProperty", preferOntologies = c("RO"))
+
    #> [1] "http://purl.obolibrary.org/obo/RO_0002202"
    term_iri("anatomical structure", firstOnly = FALSE)
+
    #> [1] "http://purl.obolibrary.org/obo/UBERON_0000061"
 #> [2] "http://purl.obolibrary.org/obo/CARO_0000003"  
    
   
    
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