diff scripts/raceID_diffgenes.R @ 0:e01c989c7543 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/raceID_diffgenes.R	Sat Mar 03 17:34:16 2018 -0500
@@ -0,0 +1,50 @@
+#!/usr/bin/env Rscript
+
+args = commandArgs(trailingOnly=T)
+
+script_dir = args[1]
+config_file = args[2]
+
+                                        # Load libs, common functions, source RaceID,
+                                        # Galaxy Params, and read input data (sc)
+source(paste(script_dir, "common.R", sep="/"))
+
+                                        # Read input data
+message("Count matrix with %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2])
+
+cdiff <- clustdiffgenes(sc, pvalue=c_pval)
+
+if (generate_extable){
+                                        # differentially expressed genes in cluster
+
+    if (!(dir.exists(outtable_dir))){
+        dir.create(outtable_dir)
+    }
+    
+    for ( n in names(cdiff) ){
+        write.table(
+            data.frame(
+                GENEID=rownames(cdiff[[n]]),
+                cdiff[[n]]
+            ),
+            paste(outtable_dir, "/gdiff", "_", n, ".tsv", sep=""),  # gdiff_cl.n.tsv
+            row.names=FALSE,
+            col.names=TRUE,
+            sep="\t",
+            quote=FALSE
+        )        
+    }
+}
+
+if (compare_clusters){   
+    clust1 <- c(unlist(lapply(strsplit(clust1, "\\s*,\\s*"), as.integer)))
+    clust2 <- c(unlist(lapply(strsplit(clust2, "\\s*,\\s*"), as.integer)))
+
+    if (length(clust1) == 1){ clust1 <- clust1[[1]] }
+    if (length(clust2) == 1){ clust2 <- clust2[[1]] }
+
+    message("Performing diffgenes with cl1=%s, cl2=%s, mincount=%.0f, gene='%s'", clust1, clust2, mcount, gene_name)
+    d <- diffgenes(sc,cl1 = clust1, cl2 = clust2, mincount = mcount)
+
+    plotter("plot_diffgenes", plotdiffgenes(d,gene= gene_name))
+}