diff scripts/raceID_kmeans_heatmap.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_kmeans_heatmap.R	Sat Mar 03 17:34:16 2018 -0500
@@ -0,0 +1,40 @@
+#!/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])
+message("Performing clustering using the following parameters: metric=%s, cln=%.0f, do.gap=%.0f clustnr=%.0f, B.gap=%.0f, SE.method=%s, SE.factor=%.2f, bootnr=%.0f, rseed=%.0f", c_metric, c_cln, dogap, c_clustnr, bgap, semethod, sefactor, c_bootnr, c_rseed)
+
+sc <- clustexp(
+    sc,
+    metric=c_metric, cln=c_cln, do.gap=dogap, clustnr=c_clustnr,
+    B.gap=bgap, SE.method=semethod, SE.factor=sefactor,
+    bootnr=c_bootnr, rseed=c_rseed
+)
+
+message("Plotting images")
+plotter("plot_gap", plotgap(sc))
+plotter("plot_jaccard", plotjaccard(sc))
+plotter("plot_silhouette", plotsilhouette(sc))
+plotter("plot_clustheatmap", x <- clustheatmap(sc, final=FALSE, hmethod="single"))
+
+
+message("Finished plots")
+
+if (generate_final_rdata){
+    message("Saving SC object")
+    saveRDS(sc, output_rdat)
+}
+
+
+
+
+