adjusted createImgMap() to only plot pathways with clickable links for which...

adjusted createImgMap() to only plot pathways with clickable links for which gene information are available (for the others the .pathways/*.png files will be plotted)

common/cp_enrichment.R

@@ -585,52 +585,75 @@ pathwayName <- function(pathwayID, enrResults) enrResults %>%
 
 ## extended version with clickable links
 createImgMap <- function(plotData){
-    warning("compiling overlay toolips...")
-
-    #    cat(paste0("pathway:", plotData$pathway_id) # todo rather show the pathway name here and create anhor list on top of section
-    #    pathwayName("mmu05145", enrResults)
-    cat(paste0("<h3>", pathwayName(plotData$pathway_id, enrResults), "</h3>"))
-
-    #pngFile="mmu04015.pathview.png"
-    #plotData <- pathwayPlots[[1]]
-    #plotData <- unlist(pathwayPlots)
-    #    pathway_id=(basename(pngFile) %>% str_split_fixed("[.]", 2))[,1]
-    pngFile <- plotData$plotfile
-    stopifnot(file.exists(pngFile))
-    pathway_id = plotData$pathway_id
-
-    ## create link for image map
-    keggNodes <- plotData$plot.data.gene %>%
-    ## remove box offset
-        mutate(x = x - 22, y = y - 8) %>% ## todo does not work for non-gene elements
-        mutate(link = paste0("http://www.kegg.jp/dbget-bin/www_bget?", keggOrCode, ":", kegg.names)) %>%
-        rowwise() %>%
-        do({ curNode = .; mutate(as_df(curNode), tooltip = makeTooltip(as.integer(curNode$kegg.names)))})
-
-    ## create tooltip by using mapping to
-
-
-    #    "http://www.kegg.jp/dbget-bin/www_bget?mmu:16412
-
-    ## first the image itself
-    #    cat(paste0("<img usemap='#", pathway_id,"' src='", pngFile, "'><br>"))
-    #    cat(paste0("<p><div style='width: 2000px'><img style='float: left' usemap='#", pathway_id,"' src='", pngFile, "'></div><br>"))
-    ## it seems that formatting works better without the left alignment
-    cat(paste0("<p><div style='width: 2000px'><img usemap='#", pathway_id, "' src='", pngFile, "'></div><br>"))
-    cat(paste0("<map name='", pathway_id, "'>"))
-    #keggNodes %>% rowwise() %>% {curNode=.; cat(curNode$name)}
-
-    #see http://www.html-world.de/180/image-map/
-    keggNodes %>% plyr::a_ply(1, function(curNode){
-        rectDef = with(curNode, paste(x, y, x + width, y + height, sep = ","))
-        #        paste0("<area href='", curNode$link, "' alt='Text' coords='", rectDef , "' shape='rect'>") %>% cat()
-        paste0("<area href='", curNode$link, "' title='", curNode$tooltip, "' alt='Text' coords='", rectDef , "' shape='rect'>") %>% cat()
-    })
-    cat("</map></p><br>")
+
+    # plots will only be rendered if they contain gene information; hsa01200 for instance is a pathway which does not reflect the genes whereas hsa05322 does
+    if (!is.null(plotData$plot.data.gene)) {
+        warning("compiling overlay toolips...")
+
+        #    cat(paste0("pathway:", plotData$pathway_id) # todo rather show the pathway name here and create anhor list on top of section
+        #    pathwayName("mmu05145", enrResults)
+        cat(paste0("<h3>", pathwayName(plotData$pathway_id, enrResults), "</h3>"))
+
+        #pngFile="mmu04015.pathview.png"
+        #plotData <- pathwayPlots[[1]]
+        #plotData <- unlist(pathwayPlots)
+        #    pathway_id=(basename(pngFile) %>% str_split_fixed("[.]", 2))[,1]
+        pngFile <- plotData$plotfile
+        stopifnot(file.exists(pngFile))
+        pathway_id = plotData$pathway_id
+
+        ## create link for image map
+        keggNodes <- plotData$plot.data.gene %>%
+        ## remove box offset
+            mutate(x = x - 22, y = y - 8) %>% ## todo does not work for non-gene elements
+            mutate(link = paste0("http://www.kegg.jp/dbget-bin/www_bget?", keggOrCode, ":", kegg.names)) %>%
+            rowwise() %>%
+            do({ curNode = .; mutate(as_df(curNode), tooltip = makeTooltip(as.integer(curNode$kegg.names)))})
+
+        ## create tooltip by using mapping to
+
+
+        #    "http://www.kegg.jp/dbget-bin/www_bget?mmu:16412
+
+        ## first the image itself
+        #    cat(paste0("<img usemap='#", pathway_id,"' src='", pngFile, "'><br>"))
+        #    cat(paste0("<p><div style='width: 2000px'><img style='float: left' usemap='#", pathway_id,"' src='", pngFile, "'></div><br>"))
+        ## it seems that formatting works better without the left alignment
+        cat(paste0("<p><div style='width: 2000px'><img usemap='#", pathway_id, "' src='", pngFile, "'></div><br>"))
+        cat(paste0("<map name='", pathway_id, "'>"))
+        #keggNodes %>% rowwise() %>% {curNode=.; cat(curNode$name)}
+
+        #see http://www.html-world.de/180/image-map/
+        keggNodes %>% plyr::a_ply(1, function(curNode){
+            rectDef = with(curNode, paste(x, y, x + width, y + height, sep = ","))
+            #        paste0("<area href='", curNode$link, "' alt='Text' coords='", rectDef , "' shape='rect'>") %>% cat()
+            paste0("<area href='", curNode$link, "' title='", curNode$tooltip, "' alt='Text' coords='", rectDef , "' shape='rect'>") %>% cat()
+        })
+        cat("</map></p><br>")
+    }
 }
 
 pathwayPlots %>% walk(createImgMap)
 
+
+#'
+#' <br>
+#'
+#' All of the following pathways (or parts of them) were found to be enriched. The hits are not visualized but can be all be found in the enrResults.txt file.
+#'
+#' <br>
+#'
+
+
+#+ results="asis", echo=FALSE, eval=hasEnrPathways
+
+invisible(lapply(1:length(pathwayPlots), function(x){
+    if (is.null(pathwayPlots[[x]]$plot.data.gene)){
+        cat("![](",paste0(".pathways/", pathwayPlots[[x]]$pathway_id,".pathview.png"),")")
+    }
+}))
+
+
 ## respin it for cild inclusion
 # require(knitr); setwd("/Volumes/projects/bioinfo/scripts/ngs_tools/dev/common"); spin("cp_enrichment.R", knit=F)