From 2c1017320e953b56f9fa5d0593f2146a88df2096 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Wed, 8 Apr 2015 16:41:53 +0200
Subject: [PATCH] added pathview species guesser
---
R/bio/diffex_commons.R | 14 ++++++++++++++
R/ggplot_commons.R | 2 +-
2 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/R/bio/diffex_commons.R b/R/bio/diffex_commons.R
index 4e5c230..b63d5af 100644
--- a/R/bio/diffex_commons.R
+++ b/R/bio/diffex_commons.R
@@ -32,6 +32,20 @@ guess_mart <- function(gene_id){
stop(paste("could not guess mart from ", an_id))
}
}
+
+guess_pathview_species <- function(gene_id){
+ an_id <-gene_id[1]
+
+ if(str_detect(an_id, "ENSMUSG")){
+ return("mmu")
+ }else if(str_detect(an_id, "ENSDARG")){
+ return("dre")
+ }else if(str_detect(an_id, "ENSG")){
+ return("hsa")
+ }else{
+ stop(paste("could not guess mart from ", an_id))
+ }
+}
#guess_mart("ENSCAFG00000000043")
diff --git a/R/ggplot_commons.R b/R/ggplot_commons.R
index a699dcd..1f8159f 100644
--- a/R/ggplot_commons.R
+++ b/R/ggplot_commons.R
@@ -149,7 +149,7 @@ makePcaPlot <- function(x = getData(), group = NA, items=rownames(x), title = ""
### Base-plot utils
-plotPDF <- function(filename, expr){ pdf(paste0(filename, ".pdf")); expr; dev.off(); }
+plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"), ...); expr; dev.off(); }
#plotPDF("test", plot(1:10))
--
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