polished separate pathway rendering

common/plot_kegg_pathways.R

@@ -42,10 +42,13 @@ require_auto(png)
 #}else{
 
 #keggOrCode <- "mmu"
-keggOrCode <- guess_pathview_species(geneLists$ensembl_gene_id)
+overlayData <- read_tsv(opts$overlay_data_tsv)
+
+keggOrCode <- guess_pathview_species(overlayData$ensembl_gene_id)
 
 ## prepare p-value data
-sliceData <- overlayData %>%
+
+sliceData <- overlayData  %>% as.df %>%
     #    dcast(ensembl_gene_id ~ comparison, value.var="plot_score") %>%
     column2rownames("ensembl_gene_id")
 
@@ -126,7 +129,7 @@ stopifnot(llply(pathwayPlots, function(x) file.exists(x$plotfile)) %>% unlist %>
 ens2entrez <- quote({
     #    mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))
     ## todo fix this https://support.bioconductor.org/p/74322/
-    mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
+    mart <- biomaRt::useDataset(guess_mart(overlayData$ensembl_gene_id), mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
 
     biomaRt::getBM(attributes=c('ensembl_gene_id', 'entrezgene', 'external_gene_name'), mart=mart) %>% filter(!is.na(entrezgene))
 }) %>% cache_it("ens2entrez") %>% distinct(ensembl_gene_id)