Mercurial > repos > iuc > ribowaltz_plot

annotate ribowaltz_plot.R @ 0:8e903cb3f919 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
author iuc
date Thu, 22 Sep 2022 20:30:20 +0000
parents
children e25d81465c23
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8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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diff changeset
1 # setup R error handling to go to stderr
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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2 options(show.error.messages = FALSE, error = function() {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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3 cat(geterrmessage(), file = stderr())
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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4 q("no", 1, FALSE)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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5 })
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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6
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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9 library("getopt")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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10 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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11 args <- commandArgs(trailingOnly = TRUE)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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12
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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13 # get options, using the spec as defined by the enclosed list.
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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14 # we read the options from the default: commandArgs(TRUE).
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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15 spec <- matrix(c(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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16 "quiet", "q", 0, "logical",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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17 "help", "h", 0, "logical",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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18 "input_rdata", "i", 1, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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19 "params_rlength_distr", "r", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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20 "params_rends_heat", "e", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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21 "region_psite_plot", "R", 0, "logical",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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22 "params_trint_periodicity", "t", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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23 "params_metaplots", "m", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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24 "params_codon_usage_psite", "u", 0, "character"
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25 ), byrow = TRUE, ncol = 4)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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26 opt <- getopt(spec)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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27
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28 # if help was asked for print a friendly message
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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29 # and exit with a non-zero error code
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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30 if (!is.null(opt$help)) {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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31 cat(getopt(spec, usage = TRUE))
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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32 q(status = 1)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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33 }
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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34
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35 verbose <- is.null(opt$quiet)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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36
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37 library("riboWaltz")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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38 library("jsonlite")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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39
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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40 load(opt$input_rdata)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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41
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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42 if (!is.null(opt$params_rlength_distr)) {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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43 pdf("read_lengths.pdf")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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44 json_rlength_distr <- fromJSON(opt$params_rlength_distr)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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45 length_dist <- rlength_distr(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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46 reads_psite_list,
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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47 sample = names(reads_psite_list),
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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48 cl = json_rlength_distr$cl,
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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49 multisamples = json_rlength_distr$multisamples,
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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50 plot_style = json_rlength_distr$plot_style
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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51 )
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52 print(length_dist)
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53 dev.off()
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54 }
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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55
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56 if (!is.null(opt$params_rends_heat)) {
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57 pdf("read_ends_heatmap.pdf", height = 5 * length(reads_psite_list), width = 15)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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58 json_rends_heat <- fromJSON(opt$params_rends_heat)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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59 for (sample_name in names(reads_psite_list)) {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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60 ends_heatmap <- rends_heat(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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61 reads_psite_list,
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62 annotation_dt,
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63 sample = sample_name,
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64 cl = json_rends_heat$cl,
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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65 utr5l = json_rends_heat$utr5l,
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66 cdsl = json_rends_heat$cdsl,
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67 utr3l = json_rends_heat$utr3l
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68 )
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69 print(ends_heatmap[["plot"]])
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70 }
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71 dev.off()
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72 }
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73
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74 if (!is.null(opt$region_psite_plot)) {
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75 pdf("psites_per_region.pdf", height = 12, width = 7 * length(reads_psite_list))
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76 psite_region <- region_psite(reads_psite_list, annotation_dt, sample = names(reads_psite_list))
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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77 print(psite_region[["plot"]])
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78 dev.off()
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79 }
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80
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81 if (!is.null(opt$params_trint_periodicity)) {
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82 pdf("trinucleotide_periodicity.pdf", height = 6 * length(reads_psite_list), width = 10)
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83 json_trint_periodicity <- fromJSON(opt$params_trint_periodicity)
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84 frames_stratified <- frame_psite_length(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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85 reads_psite_list,
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86 sample = names(reads_psite_list),
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87 cl = json_trint_periodicity$cl,
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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88 region = json_trint_periodicity$region,
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89 length_range = json_trint_periodicity$length_range
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90 )
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91 frames_stratified[["plot"]]
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92 frames <- frame_psite_length(
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93 reads_psite_list,
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94 sample = names(reads_psite_list),
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95 region = json_trint_periodicity$region,
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96 length_range = json_trint_periodicity$length_range
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97 )
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98 print(frames[["plot"]])
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99 dev.off()
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100 }
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101
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102 if (!is.null(opt$params_metaplots)) {
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103 pdf("metaplots.pdf", height = 5 * length(reads_psite_list), width = 24)
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104 json_metaplots <- fromJSON(opt$params_metaplots)
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105 metaprofile <- metaprofile_psite(
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106 reads_psite_list,
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107 annotation_dt,
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108 sample = names(reads_psite_list),
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109 multisamples = json_metaplots$multisamples,
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110 plot_style = json_metaplots$plot_style,
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111 length_range = json_metaplots$length_range,
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112 frequency = json_metaplots$frequency,
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113 utr5l = json_metaplots$utr5l,
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114 cdsl = json_metaplots$cdsl,
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115 utr3l = json_metaplots$utr3l,
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116 plot_title = "sample.transcript.length_range"
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117 )
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118 print(metaprofile)
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119 sample_list <- list()
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120 for (sample_name in names(reads_psite_list)) {
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121 sample_list[[sample_name]] <- c(sample_name)
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122 }
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123 metaheatmap <- metaheatmap_psite(
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124 reads_psite_list,
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125 annotation_dt,
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126 sample = sample_list,
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127 length_range = json_metaplots$length_range,
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128 utr5l = json_metaplots$utr5l,
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129 cdsl = json_metaplots$cdsl,
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130 utr3l = json_metaplots$utr3l,
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131 plot_title = "Comparison metaheatmap"
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132 )
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133 print(metaheatmap[["plot"]])
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134 dev.off()
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135 }
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136
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137 if (!is.null(opt$params_codon_usage_psite)) {
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138 pdf("codon_usage.pdf", height = 6, width = 16)
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139 json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
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140 for (sample_name in names(reads_psite_list)) {
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141 cu_barplot <- codon_usage_psite(
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142 reads_psite_list,
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143 annotation_dt,
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144 sample = sample_name,
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145 fastapath = json_codon_usage_psite$fastapath,
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146 fasta_genome = FALSE,
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147 frequency_normalization = json_codon_usage_psite$frequency
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148 )
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149 print(cu_barplot[["plot"]])
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150 }
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151 dev.off()
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152 }