diff scripts/raceID_outlierdetect.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_outlierdetect.R	Sat Mar 03 17:34:16 2018 -0500
@@ -0,0 +1,45 @@
+#!/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("Detecting outliers using the following parameters: outminc=%.0f, outlg=%.0f, probthr=%.0f outdistquant=%.0f", c_outminc, c_outlg, c_probthr, c_outdistquant)
+
+sc <- findoutliers(
+    sc, outminc=c_outminc, outlg=c_outlg, probthr=c_probthr,
+    thr=2**-(1:40), outdistquant=c_outdistquant
+)
+
+message("Plotting images")
+plotter("plot_background", plotbackground(sc))
+plotter("plot_sensitivity", plotsensitivity(sc))
+plotter("plot_outlierprobs", plotoutlierprobs(sc))
+plotter("plot_finalheat", y <- clustheatmap(sc,final=TRUE,hmethod="single"))
+
+
+message("Finished plots")
+
+message("Generating data tables")
+x <- data.frame( CELLID=names(sc@cpart), cluster=sc@cpart )
+write.table(
+    x[order(x$cluster,decreasing=FALSE),], output_table,
+    row.names=FALSE, col.names=TRUE, sep="\t", quote=FALSE
+)
+
+if (generate_final_rdata){
+    message("Saving SC object")
+    saveRDS(sc, output_rdat)
+}
+
+
+
+
+