--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/raceID_tsne.R	Sat Mar 03 17:33:56 2018 -0500
@@ -0,0 +1,47 @@
+##!/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])
+
+sc <- comptsne(sc,rseed = c_rseed)
+
+message("Plotting initial and final tSNEs")
+
+plotter("plot_initial", plottsne(sc,final = F))
+plotter("plot_final", plottsne(sc,final = T))
+
+if (gene_sets != "" ){
+####all_sets <- strsplit(gene_sets, "+?\\s*__split__\\s*,?")
+    all_sets <- strsplit(gene_sets, '\\s*\\+?\\s*_split_\\s*,?')
+    print(all_sets)
+
+    for (given in all_sets){
+        given <- trimws(given)
+        message("Plotting %s", given)
+        g <- c(unlist(strsplit(given,'\\s*\\+\\s*')))
+        plotter(paste("plot", given, sep="_"), plotexptsne(sc,g, n=given, logsc=T))
+    }
+}
+
+
+if (regex_val != ""){
+    message("using subcell groups")
+    plotter("plot_labels", plotlabelstsne(sc, labels = sub(regex_val, "", names(sc@ndata))))
+    plotter("plot_symbols", plotsymbolstsne(sc, types = sub(regex_val, "", names(sc@ndata))))
+} else {
+    message("using all cell ids")
+    plotter("plot_labels", plotlabelstsne(sc, labels = names(sc@ndata)))
+    plotter("plot_symbols", plotsymbolstsne(sc, types = names(sc@ndata)))
+}
+
+message("Saving SC object")
+saveRDS(sc, output_rdat)