# HG changeset patch
# User proteore
# Date 1542038065 18000
# Node ID da82872f5c80adb17f3998031a5127ed248ffc3e
# Parent  be8115c73b0d65782399777624e97808e27507b4
planemo upload commit 63302cb49d4f0f4dbc9ae141d20704822588f54e-dirty

diff -r be8115c73b0d -r da82872f5c80 kegg_pathways_visualization.R
--- a/kegg_pathways_visualization.R	Fri Nov 09 05:22:50 2018 -0500
+++ b/kegg_pathways_visualization.R	Mon Nov 12 10:54:25 2018 -0500
@@ -64,6 +64,11 @@
   return(x)
 }
 
+kegg_to_geneID <- function(vector){
+  vector <- sapply(vector, function(x) unlist(strsplit(x,":"))[2],USE.NAMES = F)
+  return (vector)
+}
+
 clean_bad_character <- function(string)  {
   string <- gsub("X","",string)
   return(string)
@@ -79,7 +84,7 @@
 #return a summary from the mapping with pathview in a vector
 mapping_summary <- function(pv.out,species,id,id_type){
   
-  mapped <- pv.out$plot.data.gene$kegg.names[which(pv.out$plot.data.gene$all.mapped!='')]
+  mapped <- unique(pv.out$plot.data.gene$kegg.names[which(pv.out$plot.data.gene$all.mapped!='')])
   nb_mapped <- length(mapped)
   nb_kegg_id <- length(unique(pv.out$plot.data.gene$kegg.names))
   ratio = round((nb_mapped/nb_kegg_id)*100, 2)
@@ -87,11 +92,11 @@
   pathway_id = paste(species,id,sep="")
   pathway_name = as.character(pathways_list[pathways_list[,1]==pathway_id,][2])
   
-  if (id_type=="geneid"){
+  if (id_type=="geneid" || id_type=="keggid") {
     row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_kegg_id,nb_mapped,ratio,paste(mapped,collapse=";"))
     names(row) <- c("KEGG pathway ID","pathway name","nb of Entrez gene ID used","nb of Entrez gene ID mapped",
                     "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped")
-  }else if (id_type=="uniprotid"){
+  } else if (id_type=="uniprotid") {
     row <- c(pathway_id,pathway_name,length(unique(uniprotID)),length(unique(geneID)),nb_mapped,nb_kegg_id,ratio,paste(mapped,collapse=";"),paste(mapped2geneID[which(mapped2geneID[,2] %in% mapped)],collapse=";"))
     names(row) <- c("KEGG pathway ID","pathway name","nb of Uniprot_AC used","nb of Entrez gene ID used","nb of Entrez gene ID mapped",
                     "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped","uniprot_AC mapped")
@@ -194,12 +199,16 @@
   }
 }
 
-##### map uniprotID to entrez geneID
+##### map uniprotID to entrez geneID and kegg to geneID
 if (id_type == "uniprotid") {
   uniprotID = tab[,ncol]
   mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
   geneID = mapped2geneID[,2]
   tab = cbind(tab,geneID)
+}else if (id_type == "keggid"){
+  keggID = tab[,ncol]  
+  geneID = kegg_to_geneID(keggID)
+  tab = cbind(tab,geneID)
 }else if (id_type == "geneid"){
   colnames(tab)[ncol] <- "geneID"
 }
diff -r be8115c73b0d -r da82872f5c80 kegg_pathways_visualization.xml
--- a/kegg_pathways_visualization.xml	Fri Nov 09 05:22:50 2018 -0500
+++ b/kegg_pathways_visualization.xml	Mon Nov 12 10:54:25 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.09.1">
+<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.12">
     <description>map visualisation (PathView)</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
@@ -148,7 +148,7 @@
         <param name="id_type" type="select" label="Select your identifiers type :">
             <option value="uniprotID">Uniprot Accession number</option>
             <option value="geneID">Entrez gene ID</option>
-            <!--option value="keggid">KEGG genes ID</option-->
+            <option value="keggid">KEGG genes ID</option>
         </param>
         <conditional name="input" >
             <param name="ids" type="select" label="Enter your identifiers (Uniprot AC or Entrez gene ID)" help="Copy/paste or ID list from a file (e.g. table)" >