resolve warning

noriakis · Apr 7, 2024 · 38f4b23 · 38f4b23
1 parent 9dc6e63
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Showing 5 changed files with 25 additions and 16 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,7 +11,6 @@ Depends:
 Imports: tm, dplyr, GeneSummary, wordcloud, cowplot, ggplotify, stopwords, ggraph, igraph, ggdendro, AnnotationDbi, patchwork, org.Hs.eg.db, jsonlite, gridExtra, pvclust, rentrez, GetoptLong, grid, grDevices, stats, NLP, bugsigdbr, stringr, XML, methods, dendextend, RColorBrewer, utils, ggrepel, cyjShiny, graphlayouts, ggforce, ggwordcloud, MASS, tidygraph, data.table, shadowtext
 Suggests:
     concaveman,
-    clusterProfiler,
     png,
     limma,
     knitr,
@@ -20,7 +19,7 @@ Suggests:
     testthat (>= 3.0.0),
     BiocStyle
 Enhances:
-    ReactomePA, Seurat, scater, pubmedMini, ggtree, quanteda, taxonomizr, udpipe
+    ReactomePA, Seurat, scater, pubmedMini, ggtree, quanteda, taxonomizr, udpipe, clusterProfiler
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Config/testthat/edition: 3

diff --git a/NAMESPACE b/NAMESPACE
@@ -64,7 +64,6 @@ export(tag_words)
 export(textORA)
 exportMethods(getSlot)
 import(GeneSummary)
-import(XML)
 import(bugsigdbr)
 import(ggplot2)
 import(ggraph)
@@ -84,6 +83,11 @@ importFrom(GetoptLong,qqcat)
 importFrom(MASS,cov.trob)
 importFrom(NLP,ngrams)
 importFrom(NLP,words)
+importFrom(XML,xmlElementsByTagName)
+importFrom(XML,xmlParse)
+importFrom(XML,xmlTreeParse)
+importFrom(XML,xmlValue)
+importFrom(XML,xpathSApply)
 importFrom(cowplot,as_grob)
 importFrom(cyjShiny,dataFramesToJSON)
 importFrom(data.table,fread)

diff --git a/R/bugsigdb.R b/R/bugsigdb.R
@@ -8,7 +8,7 @@
 #' @import wordcloud
 #' @import igraph
 #' @import ggraph ggplot2
-#' @import XML
+#' @importFrom XML xmlParse xpathSApply xmlTreeParse xmlElementsByTagName xmlValue
 #' @importFrom dplyr filter
 #' @importFrom stats dist
 #' @importFrom grDevices palette

diff --git a/R/utils.R b/R/utils.R
@@ -14,7 +14,11 @@ split_by_ea <- function(args) {
     	geneList <- args$geneList
     }
     if (args$splitByEA=="kegg") {
-    	enr_res <- clusterProfiler::enrichKEGG(geneList)
+        if (requireNamespace("clusterProfiler")) {
+            enr_res <- clusterProfiler::enrichKEGG(geneList)        
+        } else {
+            stop("Please install clusterProfiler.")
+        }
     } else {
       if (requireNamespace("ReactomePA")) {
         enr_res <- ReactomePA::enrichPathway(geneList)

diff --git a/vignettes/basic_usage_of_biotextgraph.Rmd b/vignettes/basic_usage_of_biotextgraph.Rmd
@@ -107,15 +107,6 @@ hCNet <- refseq(keggList$`05160`, plotType="network",
 plotNet(hCNet, asis=TRUE)
 ```
 
-The summarization of text in enrichment analysis results can be performed by `enrich` option. The below example shows enrichment analysis of KEGG database.
-
-```{r basic5, warning=FALSE, message=FALSE, cache=TRUE, fig.height=8, fig.width=8}
-hCNetK <- refseq(keggList$`05160`, enrich="kegg", keyType="ENTREZID",cooccurrence = TRUE,
-                           topPath=50, numWords=50, autoThresh=FALSE,
-                           plotType="network", corThresh=0.1)
-plotNet(hCNetK, asis=TRUE)
-```
-
 We create another `biotext` object to compare with.
 
 ```{r basic6, warning=FALSE, message=FALSE, cache=TRUE, fig.height=8, fig.width=8}
@@ -125,11 +116,22 @@ ecoli <- refseq(keggList$`05130`, keyType="ENTREZID", autoThresh=FALSE)
 Comparison of networks can be performed by `compareWordNet`. By providing multiple biotext class objects, it is possible to create a new network by integrating the networks and tag information contained in each object. This makes it possible to compare multiple different IDs.
 
 ```{r compare_word_net, warning=FALSE, message=FALSE, cache=TRUE, fig.height=15, fig.width=15}
-compareWordNet(list(hCNet, hCNetK, ecoli),
-               titles=c("RefSeq_05160","KEGG_05160","RefSeq_05130"),
+compareWordNet(list(hCNet, ecoli),
+               titles=c("RefSeq_05160","RefSeq_05130"),
                colPal = "Dark2") |> plotNet()
 ```
 
+The summarization of text in enrichment analysis results can be optionally performed by `enrich` option. The below example shows enrichment analysis of KEGG database.
+
+```{r basic5, warning=FALSE, message=FALSE, cache=TRUE, fig.height=8, fig.width=8}
+if (requireNamespace("clusterProfiler")) {
+    hCNetK <- refseq(keggList$`05160`, enrich="kegg", keyType="ENTREZID",cooccurrence = TRUE,
+                               topPath=50, numWords=50, autoThresh=FALSE,
+                               plotType="network", corThresh=0.1)
+    plotNet(hCNetK, asis=TRUE)    
+}
+```
+
 ## Summarizing other identifiers' data
 
 Other than genes, microbial information can also be summarized in the similar manner. For obtaining and summarizing information on disease relationship, enzymes, metabolites, and biological pathways, please refer to the [documentation](https://noriakis.github.io/software/biotextgraph). Furthermore, a manual function (`manual`) is available that performs similar operations based on customized user input.