annotate 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
author iuc
date Sat, 03 Mar 2018 17:34:16 -0500
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e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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1 #!/usr/bin/env Rscript
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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3 args = commandArgs(trailingOnly=T)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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5 script_dir = args[1]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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6 config_file = args[2]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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8 # Load libs, common functions, source RaceID,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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9 # Galaxy Params, and read input data (sc)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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10 source(paste(script_dir, "common.R", sep="/"))
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12 # Read input data
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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13 message("Count matrix with %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2])
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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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)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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16 sc <- clustexp(
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17 sc,
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18 metric=c_metric, cln=c_cln, do.gap=dogap, clustnr=c_clustnr,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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19 B.gap=bgap, SE.method=semethod, SE.factor=sefactor,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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20 bootnr=c_bootnr, rseed=c_rseed
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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21 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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23 message("Plotting images")
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24 plotter("plot_gap", plotgap(sc))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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25 plotter("plot_jaccard", plotjaccard(sc))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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26 plotter("plot_silhouette", plotsilhouette(sc))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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27 plotter("plot_clustheatmap", x <- clustheatmap(sc, final=FALSE, hmethod="single"))
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30 message("Finished plots")
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32 if (generate_final_rdata){
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33 message("Saving SC object")
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34 saveRDS(sc, output_rdat)
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35 }
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