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annotate test-data/expressionplot.txt @ 0:e462121e8269 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:27:38 -0500
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e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1
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2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
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3 Copyright (C) 2014 The R Foundation for Statistical Computing
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4 Platform: x86_64-unknown-linux-gnu (64-bit)
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5
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6 R is free software and comes with ABSOLUTELY NO WARRANTY.
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7 You are welcome to redistribute it under certain conditions.
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8 Type 'license()' or 'licence()' for distribution details.
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9
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10 Natural language support but running in an English locale
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12 R is a collaborative project with many contributors.
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13 Type 'contributors()' for more information and
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14 'citation()' on how to cite R or R packages in publications.
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16 Type 'demo()' for some demos, 'help()' for on-line help, or
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17 'help.start()' for an HTML browser interface to help.
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18 Type 'q()' to quit R.
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20 > ## Feature Selection ##
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21 > get_features <- function(myGenes, f="gene") {
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22 + if (f == "isoforms")
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23 + return(isoforms(myGenes))
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24 + else if (f == "tss")
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25 + return(TSS(myGenes))
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26 + else if (f == "cds")
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27 + return(CDS(myGenes))
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28 + else
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29 + return(myGenes)
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30 + }
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31 >
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32 > ## Main Function ##
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33 >
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34 > library(argparse)
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35 Loading required package: proto
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36 >
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37 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
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38 >
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39 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
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40 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
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41 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
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42 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
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43 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
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44 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
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45 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
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46 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
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47 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
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48 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
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49 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
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50 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
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51 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
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52 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
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53 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
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54 > parser$add_argument('--features', dest='features', action="store", default="genes")
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55 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
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56 > parser$add_argument('--iter_max', dest='iter_max', action="store")
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57 > parser$add_argument('--genes', dest='genes', action="append")
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58 > parser$add_argument('--k', dest='k', action="store")
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59 > parser$add_argument('--x', dest='x', action="store")
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60 > parser$add_argument('--y', dest='y', action="store")
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61 >
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62 > args <- parser$parse_args()
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63 >
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64 > print(args)
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65 $border
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66 [1] FALSE
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67
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68 $clustering
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69 [1] "both"
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70
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71 $count
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72 [1] FALSE
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73
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74 $error_bars
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75 [1] TRUE
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76
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77 $features
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78 [1] "gene"
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79
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80 $filename
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81 [1] "plot-expressionplot-0.png"
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82
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83 $gene_selector
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84 [1] FALSE
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85
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86 $genes
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87 [1] "XLOC_000059"
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
88
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
89 $height
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
90 [1] 960
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
91
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
92 $input_database
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
93 [1] "/tmp/tmpNZmIuK/tmpbebRiN/database/files/000/dataset_94.dat"
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
94
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
95 $iter_max
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
96 NULL
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
97
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
98 $k
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
99 NULL
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
100
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
101 $labcol
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
102 [1] FALSE
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
103
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
104 $labrow
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
105 [1] FALSE
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
106
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
107 $log10
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
108 [1] TRUE
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
109
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
110 $plotType
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
111 [1] "expressionplot"
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
112
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
113 $replicates
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
114 [1] TRUE
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
115
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
116 $smooth
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
117 [1] FALSE
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
118
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
119 $summary
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
120 [1] FALSE
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
121
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
122 $width
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
123 [1] 1280
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
124
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
125 $x
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
126 NULL
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
127
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
128 $y
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
129 NULL
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
130
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
131 >
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
132 > #q()
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
133 >
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
134 > ## Load cummeRbund library
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
135 > library("cummeRbund")
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
136 Loading required package: BiocGenerics
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
137 Loading required package: parallel
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
138
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
139 Attaching package: ‘BiocGenerics’
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
140
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
141 The following objects are masked from ‘package:parallel’:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
142
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
144 clusterExport, clusterMap, parApply, parCapply, parLapply,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
145 parLapplyLB, parRapply, parSapply, parSapplyLB
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
146
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
147 The following object is masked from ‘package:stats’:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
148
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
149 xtabs
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
150
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
151 The following objects are masked from ‘package:base’:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
152
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
157 rownames, sapply, setdiff, sort, table, tapply, union, unique,
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
158 unlist, unsplit
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
159
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
160 Loading required package: RSQLite
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
161 Loading required package: DBI
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
162 Loading required package: ggplot2
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
163 Loading required package: reshape2
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
164 Loading required package: fastcluster
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
165
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
166 Attaching package: ‘fastcluster’
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
167
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
168 The following object is masked from ‘package:stats’:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
169
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
170 hclust
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
171
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
172 Loading required package: rtracklayer
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
173 Loading required package: GenomicRanges
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
174 Loading required package: S4Vectors
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
175 Loading required package: stats4
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
176 Loading required package: IRanges
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
177 Loading required package: GenomeInfoDb
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
178 Loading required package: Gviz
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
179 Loading required package: grid
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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180
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
181 Attaching package: ‘cummeRbund’
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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182
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183 The following object is masked from ‘package:GenomicRanges’:
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184
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185 promoters
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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186
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187 The following object is masked from ‘package:IRanges’:
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188
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189 promoters
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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190
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191 The following object is masked from ‘package:BiocGenerics’:
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192
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193 conditions
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194
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195 >
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196 > ## Initialize cuff object
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197 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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198 >
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199 > ## Print out info
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200 > print(cuff)
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201 CuffSet instance with:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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202 2 samples
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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203 87 genes
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204 90 isoforms
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205 88 TSS
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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206 0 CDS
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207 87 promoters
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208 88 splicing
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209 0 relCDS
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210 > sink("cuffdb_info.txt")
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211 > print(cuff)
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212 > print("SAMPLES:")
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213 > samples(cuff)
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214 > print("REPLICATES:")
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215 > replicates(cuff)
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216 > print("FEATURES:")
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217 > print(annotation(genes(cuff)))
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218 > cat(annotation(genes(cuff))[[1]],sep=",")
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219 > sink()
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220 >
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221 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
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222 > tryCatch({
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223 + if (args$plotType == 'density') {
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224 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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225 + }
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226 + else if (args$plotType == 'boxplot') {
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227 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
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228 + }
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229 + else if (args$plotType == 'mds') {
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230 + MDSplot(genes(cuff), replicates=args$replicates)
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231 + }
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232 + else if (args$plotType == 'pca') {
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233 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
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234 + }
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235 + else if (args$plotType == 'dendrogram') {
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236 + csDendro(genes(cuff), replicates=args$replicates)
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237 + }
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238 + else if (args$plotType == 'scatter') {
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239 + if (args$gene_selector) {
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240 + myGenes <- getGenes(cuff, args$genes)
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241 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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242 + }
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243 + else {
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244 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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245 + }
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246 + }
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247 + else if (args$plotType == 'volcano') {
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248 + if (args$gene_selector) {
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249 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
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250 + }
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251 + else {
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252 + myGenes <- genes(cuff)
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253 + }
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254 + csVolcano(myGenes, args$x, args$y)
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255 + }
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256 + else if (args$plotType == 'heatmap') {
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257 + if (args$gene_selector) {
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258 + myGenes <- getGenes(cuff, args$genes)
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259 + }
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260 + else {
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261 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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262 + }
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263 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
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264 + }
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265 + else if (args$plotType == 'cluster') {
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266 + myGenes <- getGenes(cuff, args$genes)
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267 + csCluster(get_features(myGenes, args$features), k=args$k)
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268 + }
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269 + else if (args$plotType == 'dispersion') {
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270 + dispersionPlot(genes(cuff))
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271 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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272 + else if (args$plotType == 'fpkmSCV') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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273 + fpkmSCVPlot(genes(cuff))
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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274 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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275 + else if (args$plotType == 'scatterMatrix') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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276 + csScatterMatrix(genes(cuff))
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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277 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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278 + else if (args$plotType == 'expressionplot') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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279 + myGenes <- getGenes(cuff, args$genes)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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280 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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281 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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282 + else if (args$plotType == 'expressionbarplot') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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283 + myGeneId <- args$genes
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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284 + myGenes <- getGenes(cuff, myGeneId)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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285 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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286 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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287 + else if (args$plotType == 'mds') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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288 + MDSplot(genes(cuff),replicates=args$replicates)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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289 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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290 + else if (args$plotType == 'pca') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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291 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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292 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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293 + else if (args$plotType == 'maplot') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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294 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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295 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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296 + else if (args$plotType == 'genetrack') {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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297 + myGene <- getGene(cuff, args$genes)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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298 + plotTracks(makeGeneRegionTrack(myGene))
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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299 + }
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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300 + },error = function(e) {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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301 + write(paste("Failed:", e, sep=" "), stderr())
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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302 + q("no", 1, TRUE)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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303 + })
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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304 Getting gene information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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305 FPKM
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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306 Differential Expression Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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307 Annotation Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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308 Replicate FPKMs
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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309 Counts
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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310 Getting isoforms information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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311 FPKM
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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312 Differential Expression Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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313 Annotation Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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314 Replicate FPKMs
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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315 Counts
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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316 Getting CDS information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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317 FPKM
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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318 Differential Expression Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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319 Annotation Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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320 Replicate FPKMs
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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321 Counts
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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322 Getting TSS information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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323 FPKM
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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324 Differential Expression Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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325 Annotation Data
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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326 Replicate FPKMs
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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327 Counts
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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328 Getting promoter information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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329 distData
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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330 Getting splicing information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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331 distData
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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332 Getting relCDS information:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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333 distData
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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334 Fontconfig error: Cannot load default config file
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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335 > devname = dev.off()
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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336 >
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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337 > #end for
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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338 >