Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5
author computational-metabolomics
date Fri, 13 Sep 2024 12:23:45 +0000
parents a8842e5e75a7
children
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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diff changeset
1 library(msPurity)
9
a8842e5e75a7 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
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2 library(xcms)
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 library(optparse)
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 print(sessionInfo())
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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5 option_list <- list(
8
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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6 make_option(c("-o", "--out_dir"),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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7 type = "character", default = getwd(),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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8 help = "Output folder for resulting files [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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9 ),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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10 make_option(c("-x", "--xset_path"),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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11 type = "character", default = file.path(getwd(), "xset.rds"),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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12 help = "The path to the xcmsSet object [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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13 ),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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14 make_option("--polarity",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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15 default = NA,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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16 help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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17 ),
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18 make_option("--rsd_i_blank",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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19 default = 100,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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20 help = "RSD threshold for the blank [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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21 ),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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22 make_option("--minfrac_blank",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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23 default = 0.5,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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24 help = "minimum fraction of files for features needed for the blank [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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25 ),
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26 make_option("--rsd_rt_blank",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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27 default = 100,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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28 help = "RSD threshold for the RT of the blank [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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29 ),
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30 make_option("--ithres_blank",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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31 default = 0,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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32 help = "Intensity threshold for the blank [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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33 ),
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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34 make_option("--s2b",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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35 default = 10,
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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36 help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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37 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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38 1000/10 = 100, so sample has fold change higher than the threshold and the peak
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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39 is not considered a blank [default = %default]"
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40 ),
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41 make_option("--blank_class",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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42 default = "blank", type = "character",
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43 help = "A string representing the class that will be used for the blank.[default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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44 ),
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45 make_option("--egauss_thr",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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46 default = NA,
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47 help = "Threshold for filtering out non gaussian shaped peaks. Note this only works
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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48 if the 'verbose columns' and 'fit gauss' was used with xcms
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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49 [default = %default]"
8
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50 ),
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51 make_option("--rsd_i_sample",
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52 default = 100,
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53 help = "RSD threshold for the samples [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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54 ),
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55 make_option("--minfrac_sample",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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56 default = 0.8,
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57 help = "minimum fraction of files for features needed for the samples [default = %default]"
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58 ),
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59 make_option("--rsd_rt_sample",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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60 default = 100,
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61 help = "RSD threshold for the RT of the samples [default = %default]"
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62 ),
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63 make_option("--ithres_sample",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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64 default = 5000,
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65 help = "Intensity threshold for the sample [default = %default]"
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66 ),
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67 make_option("--grp_rm_ids",
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68 default = NA,
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69 help = "vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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70 [default = %default]"
8
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71 ),
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72 make_option("--remove_spectra",
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73 action = "store_true",
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74 help = "TRUE if flagged spectra is to be removed [default = %default]"
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75 ),
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76 make_option("--minfrac_xcms",
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77 default = 0.5,
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78 help = "minfrac for xcms grouping [default = %default]"
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79 ),
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80 make_option("--mzwid",
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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81 default = 0.001,
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82 help = "mzwid for xcms grouping [default = %default]"
a46824d13914 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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83 ),
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84 make_option("--bw",
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85 default = 5,
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86 help = "bw for xcms grouping [default = %default]"
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87 ),
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88 make_option("--temp_save",
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89 action = "store_true",
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90 help = "Assign True if files for each step saved (for testing purposes) [default = %default]"
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91 ),
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92 make_option("--samplelist", type = "character", help = "Sample list to determine the blank class")
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93 )
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94
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95 # nolint start
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96 # make_option("--multilist", action="store_true"
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97 # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided"
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98 # ),
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99 # nolint end
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100
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101 # store options
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102 opt <- parse_args(OptionParser(option_list = option_list))
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103
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104 opt <- replace(opt, opt == "NA", NA)
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105
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106 if (is.null(opt$temp_save)) {
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107 temp_save <- FALSE
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108 } else {
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109 temp_save <- TRUE
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110 }
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111
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112 if (is.null(opt$remove_spectra)) {
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113 remove_spectra <- FALSE
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114 } else {
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115 remove_spectra <- TRUE
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116 }
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117
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118
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119 print(opt)
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120
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121 # This R function can handle both XCMS object versions (so following code
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122 # no longer required - kept here for reference)
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123 # getxcmsSetObject <- function(xobject) {
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124 # # XCMS 1.x
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125 # if (class(xobject) == "xcmsSet"){
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126 # return(xobject)
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127 # }
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128 # # XCMS 3.x
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129 # if (class(xobject) == "XCMSnExp") {
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130 # # Get the legacy xcmsSet object
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131 # suppressWarnings(xset <- as(xobject, "xcmsSet"))
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132 # if (!is.null(xset@phenoData$sample_group)){
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133 # xcms::sampclass(xset) <- xset@phenoData$sample_group
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134 # }else{
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135 # xcms::sampclass(xset) <- "."
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136 # }
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137 # return(xset)
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138 # }
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139 # }
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140
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141
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142 loadRData <- function(rdata_path, name) {
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143 # loads an RData file, and returns the named xset object if it is there
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144 load(rdata_path)
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145 return(get(ls()[ls() %in% name]))
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146 }
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147
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148 xset <- loadRData(opt$xset_path, c("xset", "xdata"))
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149
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150
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151 if (is.null(opt$samplelist)) {
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152 blank_class <- opt$blank_class
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153 } else {
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154 samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
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155 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])
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156
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157 chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
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158 if (length(chosen_blank) > 1) {
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159 print("ERROR: only 1 blank is currently allowed to be used with this tool")
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160 quit()
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161 }
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162 blank_class <- as.character(chosen_blank)
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163 print(blank_class)
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164 }
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165
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166
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167
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168
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169 if (is.null(opt$multilist)) {
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170 ffrm_out <- flag_remove(xset,
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171 pol = opt$polarity,
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172 rsd_i_blank = opt$rsd_i_blank,
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173 minfrac_blank = opt$minfrac_blank,
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174 rsd_rt_blank = opt$rsd_rt_blank,
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175 ithres_blank = opt$ithres_blank,
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176 s2b = opt$s2b,
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177 ref.class = blank_class,
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178 egauss_thr = opt$egauss_thr,
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179 rsd_i_sample = opt$rsd_i_sample,
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180 minfrac_sample = opt$minfrac_sample,
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181 rsd_rt_sample = opt$rsd_rt_sample,
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182 ithres_sample = opt$ithres_sample,
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183 minfrac_xcms = opt$minfrac_xcms,
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184 mzwid = opt$mzwid,
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185 bw = opt$bw,
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186 out_dir = opt$out_dir,
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187 temp_save = temp_save,
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188 remove_spectra = remove_spectra,
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189 grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]]
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190 )
6
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191 print("flag remove finished")
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192 xset <- ffrm_out[[1]]
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193 grp_peaklist <- ffrm_out[[2]]
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194 removed_peaks <- ffrm_out[[3]]
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195
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196 save.image(file = file.path(opt$out_dir, "xset_filtered.RData"), version = 2)
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197
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198 # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
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199 peak_pth <- file.path(opt$out_dir, "peaklist_filtered.tsv")
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200 print(peak_pth)
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201 write.table(data.frame("grpid" = rownames(grp_peaklist), "ID" = rownames(grp_peaklist), grp_peaklist),
8
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202 peak_pth,
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203 row.names = FALSE, sep = "\t"
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204 )
0
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205
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206 removed_peaks <- data.frame(removed_peaks)
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207 write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),
8
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208 file.path(opt$out_dir, "removed_peaks.tsv"),
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209 row.names = FALSE, sep = "\t"
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210 )
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211 } else {
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212 # nolint start
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213 # TODO - potential for multilist analysis (e)
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214 # nolint end
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215 }