Mercurial > repos > computational-metabolomics > mspurity_dimspredictpuritysingle

annotate purityX.R @ 8:75b761fbacc0 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:05:52 +0000
parents 090775983be7
children 548fed2ef792
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e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(msPurity)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(optparse)
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3 print(sessionInfo())
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5 option_list <- list(
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6 make_option(c("--xset_path"), type = "character"),
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7 make_option(c("-o", "--out_dir"), type = "character"),
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8 make_option(c("--mzML_path"), type = "character"),
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9 make_option("--minOffset", default = 0.5),
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10 make_option("--maxOffset", default = 0.5),
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11 make_option("--ilim", default = 0.05),
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12 make_option("--iwNorm", default = "none", type = "character"),
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13 make_option("--exclude_isotopes", action = "store_true"),
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14 make_option("--isotope_matrix", type = "character"),
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15 make_option("--purityType", default = "purityFWHMmedian"),
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16 make_option("--singleFile", default = 0),
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17 make_option("--cores", default = 4),
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18 make_option("--xgroups", type = "character"),
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19 make_option("--rdata_name", default = "xset"),
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20 make_option("--camera_xcms", default = "xset"),
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21 make_option("--files", type = "character"),
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22 make_option("--galaxy_files", type = "character"),
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23 make_option("--choose_class", type = "character"),
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24 make_option("--ignore_files", type = "character"),
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25 make_option("--rtraw_columns", action = "store_true")
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26 )
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29 opt <- parse_args(OptionParser(option_list = option_list))
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30 print(opt)
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33 if (!is.null(opt$xgroups)) {
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34 xgroups <- as.numeric(strsplit(opt$xgroups, ",")[[1]])
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35 } else {
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36 xgroups <- NULL
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37 }
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40 print(xgroups)
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42 if (!is.null(opt$remove_nas)) {
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43 df <- df[!is.na(df$mz), ]
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44 }
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46 if (is.null(opt$isotope_matrix)) {
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47 im <- NULL
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48 } else {
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49 im <- read.table(opt$isotope_matrix,
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50 header = TRUE, sep = "\t", stringsAsFactors = FALSE
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51 )
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52 }
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54 if (is.null(opt$exclude_isotopes)) {
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55 isotopes <- FALSE
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56 } else {
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57 isotopes <- TRUE
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58 }
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60 if (is.null(opt$rtraw_columns)) {
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61 rtraw_columns <- FALSE
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62 } else {
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63 rtraw_columns <- TRUE
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64 }
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65
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66 loadRData <- function(rdata_path, xset_name) {
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67 # loads an RData file, and returns the named xset object if it is there
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68 load(rdata_path)
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69 return(get(ls()[ls() == xset_name]))
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70 }
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75 getxcmsSetObject <- function(xobject) {
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76 # XCMS 1.x
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77 if (class(xobject) == "xcmsSet") {
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78 return(xobject)
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79 }
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80 # XCMS 3.x
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81 if (class(xobject) == "XCMSnExp") {
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82 # Get the legacy xcmsSet object
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83 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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84 sampclass(xset) <- xset@phenoData$sample_group
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85 return(xset)
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86 }
0
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87 }
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89 target_obj <- loadRData(opt$xset_path, opt$rdata_name)
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90
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91 if (opt$camera_xcms == "camera") {
8
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92 xset <- target_obj@xcmsSet
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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93 } else {
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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94 xset <- target_obj
0
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95 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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96
8
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97 xset <- getxcmsSetObject(xset)
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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98
0
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99 print(xset)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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100
6
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101 minOffset <- as.numeric(opt$minOffset)
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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102 maxOffset <- as.numeric(opt$maxOffset)
0
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103
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104 if (opt$iwNorm == "none") {
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105 iwNorm <- FALSE
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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106 iwNormFun <- NULL
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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107 } else if (opt$iwNorm == "gauss") {
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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108 iwNorm <- TRUE
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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109 iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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110 } else if (opt$iwNorm == "rcosine") {
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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111 iwNorm <- TRUE
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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112 iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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113 } else if (opt$iwNorm == "QE5") {
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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114 iwNorm <- TRUE
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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115 iwNormFun <- msPurity::iwNormQE.5()
0
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116 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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117
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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118 print(xset@filepaths)
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119
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120 if (!is.null(opt$files)) {
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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121 updated_filepaths <- trimws(strsplit(opt$files, ",")[[1]])
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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122 updated_filepaths <- updated_filepaths[updated_filepaths != ""]
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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123 print(updated_filepaths)
6
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124 updated_filenames <- basename(updated_filepaths)
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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125 original_filenames <- basename(xset@filepaths)
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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126 update_idx <- match(updated_filenames, original_filenames)
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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127
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128 if (!is.null(opt$galaxy_files)) {
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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129 galaxy_files <- trimws(strsplit(opt$galaxy_files, ",")[[1]])
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130 galaxy_files <- galaxy_files[galaxy_files != ""]
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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131 xset@filepaths <- galaxy_files[update_idx]
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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132 } else {
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133 xset@filepaths <- updated_filepaths[update_idx]
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134 }
0
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135 }
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136
6
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137 if (!is.null(opt$choose_class)) {
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138 classes <- trimws(strsplit(opt$choose_class, ",")[[1]])
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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139
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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140 ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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141
6
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142 print("choose class")
0
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143 print(ignore_files_class)
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144 } else {
0
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145 ignore_files_class <- NA
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146 }
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147
6
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148 if (!is.null(opt$ignore_files)) {
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149 ignore_files_string <- trimws(strsplit(opt$ignore_files, ",")[[1]])
0
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150 filenames <- rownames(xset@phenoData)
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151 ignore_files <- which(filenames %in% ignore_files_string)
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152
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153 ignore_files <- unique(c(ignore_files, ignore_files_class))
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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154 ignore_files <- ignore_files[ignore_files != ""]
8
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155 } else {
6
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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156 if (anyNA(ignore_files_class)) {
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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157 ignore_files <- NULL
8
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158 } else {
0
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159 ignore_files <- ignore_files_class
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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160 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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161 }
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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162
6
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163 print("ignore_files")
0
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164 print(ignore_files)
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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165
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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166
8
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diff changeset
167 ppLCMS <- msPurity::purityX(
75b761fbacc0 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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168 xset = xset,
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diff changeset
169 offsets = c(minOffset, maxOffset),
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170 cores = opt$cores,
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171 xgroups = xgroups,
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computational-metabolomics
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172 purityType = opt$purityType,
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173 ilim = opt$ilim,
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computational-metabolomics
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diff changeset
174 isotopes = isotopes,
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diff changeset
175 im = im,
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176 iwNorm = iwNorm,
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177 iwNormFun = iwNormFun,
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178 singleFile = opt$singleFile,
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179 fileignore = ignore_files,
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180 rtrawColumns = rtraw_columns
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diff changeset
181 )
0
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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182
e96082a25ff0 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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183 dfp <- ppLCMS@predictions
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184
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185 # to make compatable with deconrank
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186 # (keep grpid for other compatibility)
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187 dfp <- data.frame("peakID"=dfp$grpid, dfp)
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188
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189 colnames(dfp)[colnames(dfp) == "median"] <- "medianPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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190 colnames(dfp)[colnames(dfp) == "mean"] <- "meanPurity"
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191 colnames(dfp)[colnames(dfp) == "sd"] <- "sdPurity"
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192 colnames(dfp)[colnames(dfp) == "stde"] <- "sdePurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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193 colnames(dfp)[colnames(dfp) == "RSD"] <- "cvPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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194 colnames(dfp)[colnames(dfp) == "pknm"] <- "pknmPurity"
090775983be7 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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195
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196 if (sum(is.na(dfp$medianPurity)) > 0) {
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197 dfp[is.na(dfp$medianPurity), ]$medianPurity <- 0
0
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198 }
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199
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200 print(head(dfp))
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201 write.table(dfp, file.path(opt$out_dir, "purityX_output.tsv"), row.names = FALSE, sep = "\t")
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202
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203 save.image(file.path(opt$out_dir, "purityX_output.RData"))