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annotate test-data/fpkmSCV.txt @ 5:78fcfc04fcfe draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3
author devteam
date Thu, 23 Feb 2017 20:24:03 -0500
parents 587c425b4e76
children
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587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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1 > get_features <- function(myGenes, f="gene") {
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2 + if (f == "isoforms")
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3 + return(isoforms(myGenes))
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4 + else if (f == "tss")
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5 + return(TSS(myGenes))
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6 + else if (f == "cds")
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7 + return(CDS(myGenes))
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8 + else
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9 + return(myGenes)
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10 + }
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11 >
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12 > ## Main Function ##
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13 >
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14 > library(argparse)
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15 Loading required package: proto
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16 >
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17 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
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18 >
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19 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
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20 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
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21 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
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22 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
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23 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
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24 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
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25 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
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26 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
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27 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
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28 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
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29 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
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30 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
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31 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
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32 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
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33 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
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34 > parser$add_argument('--features', dest='features', action="store", default="genes")
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35 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
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36 > parser$add_argument('--iter_max', dest='iter_max', action="store")
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37 > parser$add_argument('--genes', dest='genes', action="append")
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38 > parser$add_argument('--k', dest='k', action="store")
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39 > parser$add_argument('--x', dest='x', action="store")
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40 > parser$add_argument('--y', dest='y', action="store")
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41 >
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42 > args <- parser$parse_args()
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43 >
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44 > ## Load cummeRbund library
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45 > library("cummeRbund")
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46 Loading required package: BiocGenerics
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47 Loading required package: methods
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48 Loading required package: parallel
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49
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50 Attaching package: ‘BiocGenerics’
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51
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52 The following objects are masked from ‘package:parallel’:
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53
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54 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
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55 clusterExport, clusterMap, parApply, parCapply, parLapply,
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56 parLapplyLB, parRapply, parSapply, parSapplyLB
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57
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58 The following objects are masked from ‘package:stats’:
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60 IQR, mad, xtabs
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62 The following objects are masked from ‘package:base’:
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64 anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
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65 duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
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66 is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
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67 paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
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68 Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
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69 unique, unsplit, which, which.max, which.min
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71 Loading required package: RSQLite
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72 Loading required package: DBI
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73 Loading required package: ggplot2
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74 Loading required package: reshape2
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75 Loading required package: fastcluster
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76
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77 Attaching package: ‘fastcluster’
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78
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79 The following object is masked from ‘package:stats’:
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80
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81 hclust
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82
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83 Loading required package: rtracklayer
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84 Loading required package: GenomicRanges
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85 Loading required package: stats4
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86 Loading required package: S4Vectors
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88 Attaching package: ‘S4Vectors’
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90 The following objects are masked from ‘package:base’:
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92 colMeans, colSums, expand.grid, rowMeans, rowSums
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93
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94 Loading required package: IRanges
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95 Loading required package: GenomeInfoDb
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96 Loading required package: Gviz
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97 Loading required package: grid
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98 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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99 by .GlobalEnv when processing object ‘plot.index’
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100 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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101 by .GlobalEnv when processing object ‘plot.index’
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102 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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103 by .GlobalEnv when processing object ‘plot.index’
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104 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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105 by .GlobalEnv when processing object ‘plot.index’
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106 Warning: namespace ‘ensembldb’ is not available and has been replaced
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107 by .GlobalEnv when processing object ‘plot.index’
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108 Warning: namespace ‘ensembldb’ is not available and has been replaced
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109 by .GlobalEnv when processing object ‘plot.index’
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110 Warning: namespace ‘ensembldb’ is not available and has been replaced
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111 by .GlobalEnv when processing object ‘plot.index’
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112 Warning: namespace ‘ensembldb’ is not available and has been replaced
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113 by .GlobalEnv when processing object ‘plot.index’
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114 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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115 by .GlobalEnv when processing object ‘plot.index’
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116 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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117 by .GlobalEnv when processing object ‘plot.index’
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118 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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119 by .GlobalEnv when processing object ‘plot.index’
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120 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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121 by .GlobalEnv when processing object ‘plot.index’
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122 Warning: namespace ‘ensembldb’ is not available and has been replaced
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123 by .GlobalEnv when processing object ‘plot.index’
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124 Warning: namespace ‘ensembldb’ is not available and has been replaced
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125 by .GlobalEnv when processing object ‘plot.index’
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126 Warning: namespace ‘ensembldb’ is not available and has been replaced
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127 by .GlobalEnv when processing object ‘plot.index’
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128 Warning: namespace ‘ensembldb’ is not available and has been replaced
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129 by .GlobalEnv when processing object ‘plot.index’
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130 Warning: namespace ‘ensembldb’ is not available and has been replaced
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131 by .GlobalEnv when processing object ‘plot.index’
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132 Warning: namespace ‘ensembldb’ is not available and has been replaced
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133 by .GlobalEnv when processing object ‘plot.index’
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134 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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135 by .GlobalEnv when processing object ‘plot.index’
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136 Warning: namespace ‘ensembldb’ is not available and has been replaced
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137 by .GlobalEnv when processing object ‘plot.index’
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138 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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139 by .GlobalEnv when processing object ‘plot.index’
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140 Warning: namespace ‘ensembldb’ is not available and has been replaced
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141 by .GlobalEnv when processing object ‘plot.index’
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142 Warning: namespace ‘ensembldb’ is not available and has been replaced
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143 by .GlobalEnv when processing object ‘plot.index’
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144 Warning: namespace ‘ensembldb’ is not available and has been replaced
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145 by .GlobalEnv when processing object ‘plot.index’
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146 Warning: namespace ‘ensembldb’ is not available and has been replaced
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147 by .GlobalEnv when processing object ‘plot.index’
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148 Warning: namespace ‘ensembldb’ is not available and has been replaced
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149 by .GlobalEnv when processing object ‘plot.index’
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150 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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151 by .GlobalEnv when processing object ‘plot.index’
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152 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
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153 by .GlobalEnv when processing object ‘plot.index’
0
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154
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155 Attaching package: ‘cummeRbund’
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156
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157 The following object is masked from ‘package:GenomicRanges’:
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158
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159 promoters
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160
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161 The following object is masked from ‘package:IRanges’:
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162
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163 promoters
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164
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165 The following object is masked from ‘package:BiocGenerics’:
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166
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167 conditions
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168
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169 >
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170 > ## Initialize cuff object
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171 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
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172 >
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173 > ## Print out info
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174 > print(cuff)
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175 CuffSet instance with:
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176 2 samples
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177 87 genes
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178 90 isoforms
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179 88 TSS
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180 0 CDS
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181 87 promoters
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182 88 splicing
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183 0 relCDS
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184 > sink("cuffdb_info.txt")
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185 > print(cuff)
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186 > print("SAMPLES:")
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187 > samples(cuff)
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188 > print("REPLICATES:")
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189 > replicates(cuff)
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190 > print("FEATURES:")
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191 > print(annotation(genes(cuff)))
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192 > cat(annotation(genes(cuff))[[1]],sep=",")
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193 > sink()
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194 >
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195 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
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196 > tryCatch({
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197 + if (args$plotType == 'density') {
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198 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
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199 + }
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200 + else if (args$plotType == 'boxplot') {
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201 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
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202 + }
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203 + else if (args$plotType == 'mds') {
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204 + MDSplot(genes(cuff), replicates=args$replicates)
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205 + }
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206 + else if (args$plotType == 'pca') {
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207 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
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208 + }
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209 + else if (args$plotType == 'dendrogram') {
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210 + csDendro(genes(cuff), replicates=args$replicates)
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211 + }
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212 + else if (args$plotType == 'scatter') {
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213 + if (args$gene_selector) {
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214 + myGenes <- getGenes(cuff, args$genes)
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215 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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216 + }
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217 + else {
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218 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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219 + }
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220 + }
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221 + else if (args$plotType == 'volcano') {
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222 + if (args$gene_selector) {
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223 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
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224 + }
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225 + else {
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226 + myGenes <- genes(cuff)
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227 + }
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228 + csVolcano(myGenes, args$x, args$y)
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229 + }
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230 + else if (args$plotType == 'heatmap') {
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231 + if (args$gene_selector) {
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232 + myGenes <- getGenes(cuff, args$genes)
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233 + }
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234 + else {
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235 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
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236 + }
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237 + 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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238 + }
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239 + else if (args$plotType == 'cluster') {
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240 + myGenes <- getGenes(cuff, args$genes)
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241 + csCluster(get_features(myGenes, args$features), k=args$k)
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242 + }
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243 + else if (args$plotType == 'dispersion') {
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244 + dispersionPlot(genes(cuff))
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245 + }
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246 + else if (args$plotType == 'fpkmSCV') {
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247 + fpkmSCVPlot(genes(cuff))
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248 + }
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249 + else if (args$plotType == 'scatterMatrix') {
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250 + csScatterMatrix(genes(cuff))
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251 + }
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252 + else if (args$plotType == 'expressionplot') {
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253 + myGenes <- getGenes(cuff, args$genes)
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254 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
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255 + }
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256 + else if (args$plotType == 'expressionbarplot') {
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257 + myGeneId <- args$genes
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258 + myGenes <- getGenes(cuff, myGeneId)
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259 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
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260 + }
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261 + else if (args$plotType == 'mds') {
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262 + MDSplot(genes(cuff),replicates=args$replicates)
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263 + }
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264 + else if (args$plotType == 'pca') {
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265 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
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266 + }
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267 + else if (args$plotType == 'maplot') {
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268 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
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269 + }
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270 + else if (args$plotType == 'genetrack') {
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271 + myGene <- getGene(cuff, args$genes)
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272 + plotTracks(makeGeneRegionTrack(myGene))
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273 + }
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274 + },error = function(e) {
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275 + write(paste("Failed:", e, sep=" "), stderr())
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276 + q("no", 1, TRUE)
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277 + })
5
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278 Scale for 'x' is already present. Adding another scale for 'x', which will
78fcfc04fcfe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3
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279 replace the existing scale.
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280 `geom_smooth()` using method = 'loess'
0
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281 Warning message:
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282 In .local(object, FPKMLowerBound, ...) :
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283 At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead.
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284 > devname = dev.off()
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285 >