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ctlab · May 13, 2020 · cf2cef7 · cf2cef7
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diff --git a/_config.yml b/_config.yml
@@ -7,3 +7,7 @@ remote_theme: pmarsceill/just-the-docs
 
 kramdown:
   toc_levels: "1,2"
+
+aux_links:
+  "Phantasus on GitHub":
+      - "https://github.com/ctlab/phantasus"
diff --git a/home.md b/home.md
@@ -7,18 +7,30 @@ permalink: /
 
 # Phantasus: visual and interactive gene expression analysis
 
-This documentation describes Phantasus -- a web-application 
-for visual and interactive gene expression analysis.
-Phantasus is based on 
-[Morpheus](https://software.broadinstitute.org/morpheus/) -- a web-based software
-for heatmap visualisation and analysis, which was integrated with an R
-environment via [OpenCPU API](https://www.opencpu.org/). 
 
+This documentation describes Phantasus -- a web tool designed for visual and
+interactive gene expression analysis.
+In
+particular, it was designed to allow to go from a typical dataset to
+differential expression and downstream analysis in an easy and streamlined
+manner. For that aim, Phantasus integrates an intuitive heatmap interface with
+gene expression analysis tools from Bioconductor. 
 
-The main object in Phantasus is a gene expression matrix.
-It can either be uploaded from a local text or Excel file 
-or loaded from Gene Expression Omnibus (GEO) database by the series identifier
-(both microarray and RNA-seq datasets are supported).
-Aside from basic visualization and filtering methods as implemented in Morpheus,
-R-based methods such as k-means clustering, principal component analysis, 
-differential expression analysis with limma package are supported.  
+Main features:
+* Loading public datasets from Gene Expression Omnibus with both microarrays and RNA-seq datasets (via ARCHS4) being supported.
+* Publication ready plots with export to SVG: PCA plot, row profiles, box plots.
+* Clustering: k-means and hierarchical.
+* Gene set enrichment analysis via `fgsea` package.
+* Sharing session links.
+
+<img src="images/screenshot.png" width="600px" />
+
+Links:
+* Official mirrors: [https://ctlab.itmo.ru/phantasus](https://ctlab.itmo.ru/phantasus) 
+    and [https://artyomovlab.wustl.edu/phantasus](https://artyomovlab.wustl.edu/phantasus).
+* Source code at GitHub: [https://github.com/ctlab/phantasus](https://github.com/ctlab/phantasus). 
+* Bioconductor package: [https://bioconductor.org/packages/phantasus](https://bioconductor.org/packages/phantasus).
+* Docker image: [https://hub.docker.com/r/dzenkova/phantasus](https://hub.docker.com/r/dzenkova/phantasus).
+
+Citation:
+* Zenkova D, Kamenev V, Sablina R, Artyomov M, Sergushichev A (2018). Phantasus: visual and interactive gene expression analysis. doi: 10.18129/B9.bioc.phantasus, [https://ctlab.itmo.ru/phantasus](https://ctlab.itmo.ru/phantasus). 
diff --git a/images/gse14308_norm.png b/images/gse14308_norm.png
diff --git a/images/screenshot.png b/images/screenshot.png
diff --git a/quick-start.md b/quick-start.md
@@ -28,7 +28,7 @@ The simplest way to try Phantasus application is to go to web-site
 [https://ctlab.itmo.ru/phantasus](https://ctlab.itmo.ru/phantasus) or
 its mirror [https://artyomovlab.wustl.edu/phantasus](https://artyomovlab.wustl.edu/phantasus)
 where the latest versions are deployed. 
-Alternatively, Phantaus can be start locally (see [[Serving Phantasus]]).
+Alternatively, Phantaus can be start locally (see [Serving Phantasus](serving-phantasus.html)).
 
 When Phantasus opens the starting screen should appear:
 
@@ -55,7 +55,7 @@ Columns correspond to samples.
 They are annotated with titles, GEO sample accession identifiers and treatment field.
 The annotations, such as treatment, are loaded from user-submitted GEO annotations 
 (they can be seen, for example, in _Charateristics_
-secion at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1304836).
+section at [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1304836](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1304836)).
 We note that not for all of the datasets in GEO such proper annotations are supplied.
 
 ### Adjusting expression values
@@ -210,16 +210,13 @@ up-regulated upon LPS treatment.
 
 **Pathway analysis with FGSEA**
 
-**Note**: Self-hosted Phantasus requires additional steps to make **FGSEA** work properly:
-see section \@ref(serving-phantasus).
-
 The results of differential gene expression can be used for pathway enrichment analysis
 with _FGSEA_ tool.
 
 Open _Tools/Pathway Analysis/Perform FGSEA_, then select Pathway database, which corresponds specimen used in dataset
 (Mus Musculus in this example), ranking column and column with ENTREZID or Gene IDs.
 
-<img src="images/fgsea_tool.png" width="600px" />
+<img src="images/fgsea_tool.png" width="500px" />
 
 Clicking OK will open new tab with pathways table.
 

diff --git a/serving-phantasus.md b/serving-phantasus.md
@@ -25,8 +25,11 @@ servePhantasus()
 You can customise serving of the application by specifying following parameters:
 
 - `host` and `port` (by default: `"0.0.0.0"` and `8000`);
-- `cacheDir` (by default: `tempdir()`) -- directory where downloaded datasets will be saved and reused in later sessions;
-- `preloadedDir` (by default: `NULL`) -- directory with `ExpressionSet` objects encoded in rda-files, that can be quickly loaded to application by name (see section Preloaded datasets);
+- `cacheDir` (by default: `tempdir()`) -- directory where downloaded datasets 
+    will be saved and reused in later sessions;
+- `preloadedDir` (by default: `NULL`) -- directory with `ExpressionSet` 
+    objects encoded in rda-files, that can be quickly loaded to application by
+    name (see section [Preloaded datasets](#preloaded-datasets));
 - `openInBrowser` (by default `TRUE`).
 
 # Setting up optional features
@@ -43,6 +46,7 @@ into an RData file with `.rda` extension into a directory as specified in `serve
 
 Let us preprocess and save `GSE14308` dataset:
 
+
 ```r
 library(GEOquery)
 library(limma)
@@ -63,16 +67,15 @@ save(ess, file=file.path(preloadedDir, "GSE14308_norm.rda"))
 
 Next we can serve Phantasus with set `preloadedDir` option:
 
-```{r, eval=F}
+
+```r
 servePhantasus(preloadedDir=preloadedDir)
 ```
 
 There you can either put `GSE14308_norm` name when using open option _Saved on server datasets_ or just 
 open by specifying the name in URL: http://localhost:8000/?preloaded=GSE14308_norm.
 
-```{r, out.width="650px", echo = FALSE}
-knitr::include_graphics("images/gse14308_norm.png")
-```
+<img src="images/gse14308_norm.png" width="650px" />
 
 ## Support for RNA-seq datasets
 
@@ -83,7 +86,8 @@ the [Download](http://amp.pharm.mssm.edu/archs4/download.html) section. The
 downloaded files `human_matrix.h5` and `mouse_matrix.h5` should be placed 
 into Phantasus cache under archs4 folder.
 Or you can call
-```{r, eval=F}
+
+```r
 updateARCHS4(cacheDir=cacheDir)
 ```
 
@@ -92,11 +96,22 @@ updateARCHS4(cacheDir=cacheDir)
 
 *FGSEA* requires pathway database in `.rds` files under `<cacheDir>/fgsea` folder.
 Pathway database is an `.rds` file containing dataframe with columns: `geneID`, `pathName`, `geneSymbol`. You can see an example dataframe by entering:
-```{r, eval=TRUE}
+
+```r
 data("fgseaExample", package="phantasus")
 head(fgseaExample)
 ```
 
+```
+##   geneID                                pathName geneSymbol
+## 1  11461 5991955_Cell-cell_junction_organization       Actb
+## 2  11465 5991955_Cell-cell_junction_organization      Actg1
+## 3  12385 5991955_Cell-cell_junction_organization     Ctnna1
+## 4  12388 5991955_Cell-cell_junction_organization     Ctnnd1
+## 5  12550 5991955_Cell-cell_junction_organization       Cdh1
+## 6  12552 5991955_Cell-cell_junction_organization      Cdh11
+```
+
 ## Annotation database for AnnotationDB tool
 
 *AnnotationDB* tool requires annotation databases