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annotate signature.r @ 10:68ee7c84d498 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
author artbio
date Tue, 07 Jan 2020 06:59:56 -0500
parents a35e6f9c1d34
children 8d3ca9652a5b
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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
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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2 #options(show.error.messages=F,
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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3 #error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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4 warnings()
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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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6 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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7 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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8 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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9 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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10 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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11 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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13 option_list <- list(
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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14 make_option("--h_dataframe", type="character", help="path to h-signature dataframe"),
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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15 make_option("--z_dataframe", type="character", help="path to z-signature dataframe"),
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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16 make_option("--plot_method", type = "character", help="How data should be plotted (global or lattice)"),
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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17 make_option("--pdf", type = "character", help="path to the pdf file with plots"),
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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18 make_option("--title", type = "character", help="Graph Title")
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19 )
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21 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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22 args = parse_args(parser)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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27 # data frames implementation
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28 h_dataframe = read.delim(args$h_dataframe, header=F)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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29 colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score")
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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30 h_dataframe$sig = h_dataframe$sig * 100 # to get probs in %
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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31 z_dataframe = read.delim(args$z_dataframe, header=F)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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32 colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score")
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34 # functions
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35 globalgraph = function () {
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36 pdf(args$pdf)
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37 par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
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39 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,3)],
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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40 type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)",
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41 ylab="Numbers of pairs", col="darkslateblue", lwd=4)
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43 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,4)],
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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44 type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)",
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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45 ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2)
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47 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,3)],
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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48 type = "l", main="Overlap probabilities", cex.main=1, xlab="overlap (nt)",
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49 ylab="Probability [%]", ylim=c(0,50), pch=19, col="darkslateblue", lwd=2)
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51 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)],
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52 type = "l", main="Overlap Probability Z-scores", cex.main=1,
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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53 xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2,
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54 col="darkslateblue", lwd=2)
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56 mtext(args$title, outer = TRUE, cex=1)
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57 dev.off()
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58 }
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60 treillisgraph = function (df, ...) {
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61 pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677
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62 p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df,
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63 type = "l",
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64 col='darkblue',
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65 cex=0.5,
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66 scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)),
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67 xlab = "Overlap",
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68 ylab = "signature (Nbr of pairs / Overlap prob.)",
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69 main = args$title,
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70 par.strip.text=list(cex=.5),
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71 pch=19, lwd =2,
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72 as.table=TRUE,
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73 layout=c(2,12),
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74 newpage = T,
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75 ...)
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76 plot(p)
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77 dev.off()
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78 }
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79
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80 # main
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81
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82 if (args$plot_method=="global") {
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83 globalgraph()
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84 }
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85
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86 if(args$plot_method=="lattice") {
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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87 # rearrange dataframes
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88 h_sig = h_dataframe[,c(1,2,3)]
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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89 h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig)
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90 colnames(h_sig) = c("method", "chrom", "overlap", "sig")
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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91 z_pairs = z_dataframe[,c(1,2,3)]
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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92 z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs)
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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93 colnames(z_pairs) = c("method", "chrom", "overlap", "sig")
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94 lattice_df = rbind(z_pairs, h_sig)
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95 par.settings.treillis=list(strip.background = list(
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96 col = c("lightblue", "lightgreen")))
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97
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98 treillisgraph(lattice_df, par.settings=par.settings.treillis)
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99 }