Mercurial > repos > iuc > raceid_diffgene
comparison scripts/raceID_kmeans_heatmap.R @ 0:d6a18fea319f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
| author | iuc |
|---|---|
| date | Sat, 03 Mar 2018 17:33:01 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:d6a18fea319f |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 args = commandArgs(trailingOnly=T) | |
| 4 | |
| 5 script_dir = args[1] | |
| 6 config_file = args[2] | |
| 7 | |
| 8 # Load libs, common functions, source RaceID, | |
| 9 # Galaxy Params, and read input data (sc) | |
| 10 source(paste(script_dir, "common.R", sep="/")) | |
| 11 | |
| 12 # Read input data | |
| 13 message("Count matrix with %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2]) | |
| 14 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) | |
| 15 | |
| 16 sc <- clustexp( | |
| 17 sc, | |
| 18 metric=c_metric, cln=c_cln, do.gap=dogap, clustnr=c_clustnr, | |
| 19 B.gap=bgap, SE.method=semethod, SE.factor=sefactor, | |
| 20 bootnr=c_bootnr, rseed=c_rseed | |
| 21 ) | |
| 22 | |
| 23 message("Plotting images") | |
| 24 plotter("plot_gap", plotgap(sc)) | |
| 25 plotter("plot_jaccard", plotjaccard(sc)) | |
| 26 plotter("plot_silhouette", plotsilhouette(sc)) | |
| 27 plotter("plot_clustheatmap", x <- clustheatmap(sc, final=FALSE, hmethod="single")) | |
| 28 | |
| 29 | |
| 30 message("Finished plots") | |
| 31 | |
| 32 if (generate_final_rdata){ | |
| 33 message("Saving SC object") | |
| 34 saveRDS(sc, output_rdat) | |
| 35 } | |
| 36 | |
| 37 | |
| 38 | |
| 39 | |
| 40 |