Mercurial > repos > iuc > genomic_super_signature

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
author iuc
date Wed, 12 Jan 2022 19:07:45 +0000
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d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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diff changeset
1 suppressPackageStartupMessages(library(optparse))
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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2
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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3 ### Parsing command line -------------------------------------------------------
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iuc
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4 option_list <- list(
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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5 make_option(c("--input"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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6 default = NULL, help = "Count matrix in tsv format"),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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7 make_option(c("--model"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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8 default = NULL, help = "RAVmodel to apply.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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9 Currently 'C2' and 'PLIERpriors' are available"),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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10 make_option(c("--method"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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11 default = formals(GenomicSuperSignature::validate)$method),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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12 make_option(c("--maxFrom"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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13 default = formals(GenomicSuperSignature::validate)$maxFrom),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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14 make_option(c("--level"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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15 default = formals(GenomicSuperSignature::validate)$level),
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16 make_option(c("--scale"), type = "character",
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17 default = formals(GenomicSuperSignature::validate)$scale),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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18 make_option(c("--outDir"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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19 default = NULL, help = "Output file name"),
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20 make_option(c("--validate"), type = "character",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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21 default = NULL, help = "Path to save validate.csv"),
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22 make_option(c("--html"), type = "character",
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23 default = NULL, help = "Path to save HTML report"),
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24 make_option(c("--numOut"), type = "integer",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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25 default = 3, help = "The number of top validated RAVs to check"),
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26 make_option(c("--toolDir"), type = "character",
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27 default = ".", help = "Directory containing the tool scripts (e.g. gss.Rmd")
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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28 )
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29
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30 opt <- parse_args(OptionParser(option_list = option_list),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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31 args = commandArgs(trailingOnly = TRUE))
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32 input <- opt$input
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33 model <- opt$model
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34 out_dir <- opt$outDir
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35 num_out <- opt$numOut
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36
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37 if (is.null(input)) stop("Need --input.")
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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38 if (is.null(model)) stop("Need --model.")
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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39 if (is.null(out_dir)) stop("Need --outDir.")
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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40
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41 input_name <- basename(tools::file_path_sans_ext(input))
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42 out_dir <- normalizePath(out_dir)
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43
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44 suppressPackageStartupMessages(library(GenomicSuperSignature))
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45 dat <- as.matrix(read.table(file = input, header = TRUE, sep = "\t",
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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46 row.names = 1))
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47 if (model %in% c("C2", "PLIERpriors")) {
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48 rav_model <- getModel(model)
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49 } else {
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50 rav_model <- readRDS(model)
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51 }
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52
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53
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54
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55 ### validate -------------------------------------------------------------------
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56 val_all <- validate(dat, rav_model)
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57 validated_ind <- validatedSignatures(val_all, num.out = num_out,
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58 swCutoff = 0, indexOnly = TRUE)
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59 n <- min(num_out, length(validated_ind), na.rm = TRUE)
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60
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61 ### Save tables in csv ---------------------------------------------------------
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62 # Validation
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63 if (is.null(opt$validate)) {
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64 output_fname <- file.path(out_dir, paste0(input_name, "_validate.csv"))
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65 } else {
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66 output_fname <- opt$validate
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67 }
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68 write.csv(val_all,
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69 file = output_fname,
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70 row.names = TRUE)
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71
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72 # GSEA
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73 for (i in seq_len(n)) {
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74 rav_num <- validated_ind[i]
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75 rav_name <- paste0("RAV", rav_num)
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76 res <- gsea(rav_model)[[rav_name]]
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77
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78 output_fname <- paste0(input_name, "_genesets_RAV", rav_num, ".csv")
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79 write.csv(res,
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80 file = file.path(out_dir, output_fname),
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81 row.names = TRUE)
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82 }
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83
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84 # Related prior studies
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85 for (i in seq_len(n)) {
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86 rav_num <- validated_ind[i]
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87 res <- findStudiesInCluster(rav_model, rav_num)
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88
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89 output_fname <- paste0(input_name, "_literatures_RAV", rav_num, ".csv")
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90 write.csv(res,
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91 file = file.path(out_dir, output_fname),
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92 row.names = TRUE)
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93 }
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94
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95 ### Create a report ------------------------------------------------------------
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96 if (is.null(opt$html)) {
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97 output_fname <- file.path(out_dir, paste0("GSS-", input_name, "-",
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98 format(Sys.Date(), format = "%Y%m%d"), ".html"))
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99 } else {
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100 output_fname <- opt$html
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101
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102 }
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103 rmarkdown::render(
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104 file.path(opt$toolDir, "gss.Rmd"), params = list(
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105 val_all = val_all,
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106 dat = dat,
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107 RAVmodel = rav_model,
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108 inputName = input_name,
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109 numOut = num_out
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110 ),
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111 output_file = output_fname,
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112 intermediates_dir = ".",
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113 knit_root_dir = "."
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114 )