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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
author artbio
date Thu, 06 Apr 2023 23:00:41 +0000
parents dc862983eb98
children
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3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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1 ## Setup R error handling to go to stderr
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dc862983eb98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
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2 options(show.error.messages = FALSE,
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ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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3 error = function() {
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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4 cat(geterrmessage(), file = stderr())
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5 q("no", 1, FALSE)
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6 }
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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7 )
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3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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8 warnings()
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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10 library(RColorBrewer)
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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11 library(lattice)
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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12 library(latticeExtra)
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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13 library(grid)
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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14 library(gridExtra)
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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15 library(optparse)
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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17 option_list <- list(
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18 make_option("--h_dataframe", type = "character",
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19 help = "path to h-signature dataframe"),
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20 make_option("--z_dataframe", type = "character",
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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21 help = "path to z-signature dataframe"),
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22 make_option("--plot_method", type = "character",
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23 help = "How data should be plotted (global or lattice)"),
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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24 make_option("--pdf", type = "character", help = "path to the pdf file with plots"),
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25 make_option("--title", type = "character", help = "Graph Title"),
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27 make_option("--npairs_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Numbers-of-pairs plot"),
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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28 make_option("--npairszscore_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Number-of-pairs-Z−scores plot"),
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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29 make_option("--overlapprob_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Overlap-probabilities plot"),
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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30 make_option("--overlapprobzscore_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Overlap-probabilities-Z−scores plot")
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3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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31 )
3e0ea204d09e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
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32 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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33 args <- parse_args(parser)
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35 # data frames implementation
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36 h_dataframe <- read.delim(args$h_dataframe, header = FALSE)
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37 colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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38 h_dataframe$sig <- h_dataframe$sig * 100 # to get probs in %
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39 z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
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40 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
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41
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42 # graph limits parameters
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43 if (args$npairs_ylim == 0) {
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44 npairs_ylim <- NULL
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45 } else {
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46 npairs_ylim <- c(0, args$npairs_ylim)
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47 }
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49 if (args$npairszscore_ylim == 0) {
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50 npairszscore_ylim <- NULL
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51 } else {
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52 npairszscore_ylim <- c(0, args$npairszscore_ylim)
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53 }
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55 if (args$overlapprob_ylim == 0) {
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56 overlapprob_ylim <- NULL
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57 } else {
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58 overlapprob_ylim <- c(0, args$overlapprob_ylim)
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59 }
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61 if (args$overlapprobzscore_ylim == 0) {
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62 overlapprobzscore_ylim <- NULL
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63 } else {
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64 overlapprobzscore_ylim <- c(0, args$overlapprobzscore_ylim)
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65 }
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68 # functions
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69 globalgraph <- function() {
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70 pdf(args$pdf)
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71 par(mfrow = c(2, 2), oma = c(0, 0, 3, 0))
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73 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 3)],
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74 type = "h", main = "Numbers of pairs", cex.main = 1, xlab = "overlap (nt)",
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75 ylab = "Numbers of pairs", col = "darkslateblue", lwd = 4,
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76 ylim = npairs_ylim
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77 )
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79 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 4)],
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80 type = "l", main = "Number of pairs Z-scores", cex.main = 1, xlab = "overlap (nt)",
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81 ylab = "z-score", pch = 19, cex = 0.2, col = "darkslateblue", lwd = 2,
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82 ylim = npairszscore_ylim
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83 )
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84
4
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85 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 3)],
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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86 type = "l", main = "Overlap probabilities", cex.main = 1,
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87 xlab = "overlap (nt)",
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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88 ylab = "Probability [%]", pch = 19,
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89 col = "darkslateblue", lwd = 2,
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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90 ylim = overlapprob_ylim
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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91 )
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92
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93 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)],
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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94 type = "l", main = "Overlap Probability Z-scores", cex.main = 1,
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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95 xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2,
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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96 col = "darkslateblue", lwd = 2,
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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97 ylim = overlapprobzscore_ylim
2c448b9c0175 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
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98 )
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99
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100 mtext(args$title, outer = TRUE, cex = 1)
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101 dev.off()
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102 }
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103
1
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104 treillisgraph <- function(df, ...) {
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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105 pdf(args$pdf, paper = "special", height = 11.69, width = 6)
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106 p <- xyplot(sig ~ overlap | factor(method, levels = unique(method)) + chrom,
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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107 data = df,
0
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108 type = "l",
1
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109 col = "darkblue",
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110 cex = 0.5,
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111 scales = list(y = list(tick.number = 4, relation = "free", cex = 0.6,
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112 rot = 0),
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113 x = list(cex = 0.6, alternating = FALSE)),
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114 xlab = "Overlap",
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115 ylab = "signature (Nbr of pairs / Overlap prob.)",
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116 main = args$title,
1
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117 par.strip.text = list(cex = .5),
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118 pch = 19, lwd = 2,
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119 as.table = TRUE,
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120 layout = c(2, 12),
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121 newpage = TRUE,
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122 ...)
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123 plot(p)
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124 dev.off()
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125 }
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126
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127 # main
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128
1
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129 if (args$plot_method == "global") {
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130 globalgraph()
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131 }
0
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132
1
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133 if (args$plot_method == "lattice") {
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134 # rearrange dataframes
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135 h_sig <- h_dataframe[, c(1, 2, 3)]
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136 h_sig <- cbind(rep("Overlap Prob (%)", length(h_sig[, 1])), h_sig)
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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137 colnames(h_sig) <- c("method", "chrom", "overlap", "sig")
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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138 z_pairs <- z_dataframe[, c(1, 2, 3)]
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139 z_pairs <- cbind(rep("Nbr of pairs", length(z_pairs[, 1])), z_pairs)
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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140 colnames(z_pairs) <- c("method", "chrom", "overlap", "sig")
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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141 lattice_df <- rbind(z_pairs, h_sig)
ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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142 par_settings_treillis <- list(strip.background = list(
0
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143 col = c("lightblue", "lightgreen")))
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ca2b04cdbf4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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144 treillisgraph(lattice_df, par.settings = par_settings_treillis)
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145 }