proteore_maps_visualization: kegg_maps_visualization.R comparison

planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba

comparison

equal deleted inserted replaced

-:48f302ae5545
+:8a6863adcd09
 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
 colnames(res)=colnames(tab)
 }
 return(res)
+}
+get_limit <- function(mat) {
+min = min(apply(mat,2,min))
+max = max(apply(mat,2,max))
+return(c(min,max))
 }
 get_args <- function(){
 ## Collect arguments
 mat = tab[geneID_indices,c(ncol,fold_change)]
 mat = mat[(!duplicated(mat$geneID)),]
 geneID=mat$geneID
 mat = as.data.frame(mat[,-1])
 row.names(mat)=geneID
+limit = get_limit(mat)
 } else {
 mat = unique(as.character(tab$geneID[!is.na(tab$geneID[tab$geneID!=""])]))
 geneID=mat
+limit=1
 }
 #####mapping geneID (with or without expression values) on KEGG pathway
 plot.col.key= TRUE
 low_color = "green"
 mid_color = "#F3F781" #yellow
 high_color = "red"
 if (!fold_change_data) {
 plot.col.key= FALSE   #if there's no exrepession data, we don't show the color key
 high_color = "#81BEF7" #blue
 }
 #create graph(s) and text output
 for (id in ids) {
 suffix= get_suffix(pathways_list,species,id)
 pv.out <- suppressMessages(pathview(gene.data = mat,
 mid = list(gene = mid_color, cpd = "transparent"),
 high = list(gene = high_color, cpd = "yellow"),
 na.col="#D8D8D8", #gray
 cpd.data=NULL,
 plot.col.key = plot.col.key,
-pdf.size=c(9,9)))
+pdf.size=c(9,9),
+limit=list(gene=limit, cpd=limit)))
 if (is.list(pv.out)){
 #creating text file
 if (!exists("DF")) {

Mercurial > repos > proteore > proteore_maps_visualization