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annotate signature.r @ 13:124f404b0fe7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit bc672cf9d5fe9c1f7eaf02abdc906cf2c1763668
author artbio
date Sat, 25 Feb 2023 09:54:28 +0000
parents aa5e2c64dff8
children 5150d641d515
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a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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1 ## Setup R error handling to go to stderr
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aa5e2c64dff8 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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3 error = function() {
8d3ca9652a5b "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 }
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7 )
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a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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8 warnings()
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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10 library(RColorBrewer)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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11 library(lattice)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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12 library(latticeExtra)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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13 library(grid)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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14 library(gridExtra)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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15 library(optparse)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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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",
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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)"),
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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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26 )
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27 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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28 args <- parse_args(parser)
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30 # data frames implementation
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aa5e2c64dff8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
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31 h_dataframe <- read.delim(args$h_dataframe, header = FALSE)
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32 colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
8d3ca9652a5b "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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33 h_dataframe$sig <- h_dataframe$sig * 100 # to get probs in %
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34 z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
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35 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
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a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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37 # functions
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38 globalgraph <- function() {
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a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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39 pdf(args$pdf)
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40 par(mfrow = c(2, 2), oma = c(0, 0, 3, 0))
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41 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 3)],
8d3ca9652a5b "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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42 type = "h", main = "Numbers of pairs", cex.main = 1, xlab = "overlap (nt)",
8d3ca9652a5b "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
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43 ylab = "Numbers of pairs", col = "darkslateblue", lwd = 4)
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44
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45 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 4)],
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46 type = "l", main = "Number of pairs Z-scores", cex.main = 1, xlab = "overlap (nt)",
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47 ylab = "z-score", pch = 19, cex = 0.2, col = "darkslateblue", lwd = 2)
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49 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 3)],
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50 type = "l", main = "Overlap probabilities", cex.main = 1,
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51 xlab = "overlap (nt)",
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52 ylab = "Probability [%]", ylim = c(0, 50), pch = 19,
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53 col = "darkslateblue", lwd = 2)
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55 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)],
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56 type = "l", main = "Overlap Probability Z-scores", cex.main = 1,
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57 xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2,
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58 col = "darkslateblue", lwd = 2)
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59 mtext(args$title, outer = TRUE, cex = 1)
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60 dev.off()
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61 }
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63 treillisgraph <- function(df, ...) {
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64 pdf(args$pdf, paper = "special", height = 11.69, width = 6)
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65 p <- xyplot(sig ~ overlap | factor(method, levels = unique(method)) + chrom,
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66 data = df,
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67 type = "l",
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68 col = "darkblue",
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69 cex = 0.5,
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70 scales = list(y = list(tick.number = 4, relation = "free", cex = 0.6,
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71 rot = 0),
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72 x = list(cex = 0.6, alternating = FALSE)),
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73 xlab = "Overlap",
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74 ylab = "signature (Nbr of pairs / Overlap prob.)",
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75 main = args$title,
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76 par.strip.text = list(cex = .5),
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77 pch = 19, lwd = 2,
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78 as.table = TRUE,
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79 layout = c(2, 12),
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80 newpage = TRUE,
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81 ...)
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82 plot(p)
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83 dev.off()
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84 }
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85
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86 # main
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87
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88 if (args$plot_method == "global") {
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89 globalgraph()
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90 }
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91
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92 if (args$plot_method == "lattice") {
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93 # rearrange dataframes
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94 h_sig <- h_dataframe[, c(1, 2, 3)]
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95 h_sig <- cbind(rep("Overlap Prob (%)", length(h_sig[, 1])), h_sig)
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96 colnames(h_sig) <- c("method", "chrom", "overlap", "sig")
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97 z_pairs <- z_dataframe[, c(1, 2, 3)]
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98 z_pairs <- cbind(rep("Nbr of pairs", length(z_pairs[, 1])), z_pairs)
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99 colnames(z_pairs) <- c("method", "chrom", "overlap", "sig")
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100 lattice_df <- rbind(z_pairs, h_sig)
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101 par_settings_treillis <- list(strip.background = list(
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102 col = c("lightblue", "lightgreen")))
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103 treillisgraph(lattice_df, par.settings = par_settings_treillis)
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104 }