Mercurial > repos > artbio > cpm_tpm_rpk

annotate cpm_tpm_rpk.R @ 6:d2575928b824 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 6b0877a65bb8141d028dbff2fcf73b223d864635
author artbio
date Sat, 14 Oct 2023 16:24:48 +0000
parents bcff1eb6fdb5
children f00c1c34565e
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35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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1 if (length(commandArgs(TRUE)) == 0) {
4
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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2 system("Rscript cpm_tpm_rpk.R -h", intern = FALSE)
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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3 q("no")
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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4 }
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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5
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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6
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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7 # load packages that are provided in the conda env
4
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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8 options(show.error.messages = FALSE,
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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9 error = function() {
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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10 cat(geterrmessage(), file = stderr())
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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11 q("no", 1, FALSE)
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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12 }
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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13 )
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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14 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") # nolint⁠
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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15 warnings()
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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16 library(optparse)
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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17 library(ggplot2)
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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18 library(reshape2)
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be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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19 library(Rtsne) # nolint⁠
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20 library(ggfortify)
1
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21
0
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24 #Arguments
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25 option_list <- list(
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35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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26 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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27 c("-d", "--data"),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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28 default = NA,
4
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29 type = "character",
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35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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30 help = "Input file that contains count values to transform"
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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31 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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32 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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33 c("-t", "--type"),
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34 default = "cpm",
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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35 type = "character",
3
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36 help = "Transformation type, either cpm, tpm, rpk or none[default : '%default' ]"
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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37 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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38 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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39 c("-s", "--sep"),
4
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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40 default = "\t",
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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41 type = "character",
0
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42 help = "File separator [default : '%default' ]"
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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43 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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44 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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45 c("-c", "--colnames"),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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46 default = TRUE,
4
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
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47 type = "logical",
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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48 help = "Consider first line as header ? [default : '%default' ]"
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49 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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50 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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51 c("-f", "--gene"),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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52 default = NA,
4
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53 type = "character",
0
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54 help = "Two column of gene length file"
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55 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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56 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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57 c("-a", "--gene_sep"),
4
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58 default = "\t",
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59 type = "character",
0
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60 help = "Gene length file separator [default : '%default' ]"
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61 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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62 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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63 c("-b", "--gene_header"),
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64 default = TRUE,
4
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65 type = "logical",
0
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66 help = "Consider first line of gene length as header ? [default : '%default' ]"
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67 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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68 make_option(
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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69 c("-l", "--log"),
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70 default = FALSE,
4
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71 type = "logical",
0
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72 help = "Should be log transformed as well ? (log2(data +1)) [default : '%default' ]"
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73 ),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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74 make_option(
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75 c("-o", "--out"),
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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76 default = "res.tab",
4
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77 type = "character",
0
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78 help = "Output name [default : '%default' ]"
1
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79 ),
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80 make_option(
2
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81 "--visu",
1
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82 default = FALSE,
4
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83 type = "logical",
1
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84 help = "performs T-SNE [default : '%default' ]"
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85 ),
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diff changeset
86 make_option(
2
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87 "--tsne_labels",
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88 default = FALSE,
4
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89 type = "logical",
2
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90 help = "add labels to t-SNE plot [default : '%default' ]"
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artbio
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91 ),
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92 make_option(
1
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93 "--seed",
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94 default = 42,
4
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95 type = "integer",
1
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96 help = "Seed value for reproducibility [default : '%default' ]"
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97 ),
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98 make_option(
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99 "--perp",
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100 default = 5.0,
4
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101 type = "numeric",
1
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102 help = "perplexity [default : '%default' ]"
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103 ),
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104 make_option(
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105 "--theta",
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106 default = 1.0,
4
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107 type = "numeric",
1
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108 help = "theta [default : '%default' ]"
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109 ),
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110 make_option(
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111 c("-D", "--tsne_out"),
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112 default = "tsne.pdf",
4
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113 type = "character",
1
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114 help = "T-SNE pdf [default : '%default' ]"
2
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115 ),
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116 make_option(
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117 "--pca_out",
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118 default = "pca.pdf",
4
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119 type = "character",
2
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120 help = "PCA pdf [default : '%default' ]"
0
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121 )
2
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122
0
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123 )
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124
4
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125 opt <- parse_args(OptionParser(option_list = option_list),
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126 args = commandArgs(trailingOnly = TRUE))
0
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127
4
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128 if (opt$data == "" && !(opt$help)) {
0
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129 stop("At least one argument must be supplied (count data).\n",
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130 call. = FALSE)
4
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131 } else if ((opt$type == "tpm" || opt$type == "rpk") && opt$gene == "") {
0
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132 stop("At least two arguments must be supplied (count data and gene length file).\n",
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133 call. = FALSE)
4
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134 } else if (opt$type != "tpm" && opt$type != "rpk" && opt$type != "cpm" && opt$type != "none") {
0
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135 stop("Wrong transformation requested (--type option) must be : cpm, tpm or rpk.\n",
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136 call. = FALSE)
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137 }
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138
4
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139 if (opt$sep == "tab") {
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140 opt$sep <- "\t"
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141 }
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142 if (opt$gene_sep == "tab") {
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143 opt$gene_sep <- "\t"
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144 }
0
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145
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146 cpm <- function(count) {
4
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147 (count / colSums(count)) * 1000000
0
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148 }
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149
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150
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151 rpk <- function(count, length) {
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152 count / (length / 1000)
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153 }
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154
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155 tpm <- function(count, length) {
4
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156 rpk <- rpk(count, length)
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157 per_million_factor <- colSums(rpk) / 1000000
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158 tpm <- rpk / per_million_factor
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159 return(tpm)
0
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160 }
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161
4
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162 #### running code ####
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163
5
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164 data <- read.delim(
0
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165 opt$data,
3
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166 check.names = FALSE,
1
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167 header = opt$colnames,
0
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168 row.names = 1,
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169 sep = opt$sep
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170 )
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171
4
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172 if (opt$type == "tpm" || opt$type == "rpk") {
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173 gene_length <- as.data.frame(
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174 read.delim(
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175 opt$gene,
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176 header = opt$gene_header,
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177 row.names = 1,
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178 sep = opt$gene_sep
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179 )
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180 )
4
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181 gene_length <- as.data.frame(gene_length[match(rownames(data), rownames(gene_length)), ], rownames(data))
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182 }
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183
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184
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185 if (opt$type == "cpm")
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186 res <- cpm(data)
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187 if (opt$type == "tpm")
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188 res <- as.data.frame(apply(data, 2, tpm, length = gene_length), row.names = rownames(data))
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189 if (opt$type == "rpk")
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190 res <- as.data.frame(apply(data, 2, rpk, length = gene_length), row.names = rownames(data))
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191 if (opt$type == "none")
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192 res <- data
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193 colnames(res) <- colnames(data)
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194
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195 if (opt$log == TRUE) {
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196 res <- log2(res + 1)
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197 }
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198
4
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199 if (opt$visu == TRUE) {
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200 df <- res
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201 # filter and transpose df for tsne and pca
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202 df <- df[rowSums(df) != 0, ] # remove lines without information (with only 0 counts)
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203 tdf <- t(df)
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204 # make tsne and plot results
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205 set.seed(opt$seed) ## Sets seed for reproducibility
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206 tsne_out <- Rtsne(tdf, perplexity = opt$perp, theta = opt$theta)
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207 embedding <- as.data.frame(tsne_out$Y)
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208 embedding$Class <- as.factor(sub("Class_", "", rownames(tdf)))
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209 gg_legend <- theme(legend.position = "none")
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210 ggplot(embedding, aes(x = V1, y = V2)) +
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211 geom_point(size = 1, color = "red") +
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212 gg_legend +
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213 xlab("") +
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214 ylab("") +
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215 ggtitle("t-SNE") +
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216 if (opt$tsne_labels == TRUE) {
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217 geom_text(aes(label = Class), hjust = -0.2, vjust = -0.5, size = 2.5, color = "darkblue")
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218 }
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219 ggsave(file = opt$tsne_out, device = "pdf")
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220 # make PCA and plot result with ggfortify (autoplot)
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221 tdf_pca <- prcomp(tdf, center = TRUE, scale. = TRUE)
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222 if (opt$tsne_labels == TRUE) {
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223 autoplot(tdf_pca, shape = FALSE, label = TRUE, label.size = 2.5, label.vjust = 1.2,
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224 label.hjust = 1.2,
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225 colour = "darkblue") +
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226 geom_point(size = 1, color = "red") +
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227 xlab(paste("PC1", summary(tdf_pca)$importance[2, 1] * 100, "%")) +
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228 ylab(paste("PC2", summary(tdf_pca)$importance[2, 2] * 100, "%")) +
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229 ggtitle("PCA")
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230 ggsave(file = opt$pca_out, device = "pdf")
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231 } else {
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232 autoplot(tdf_pca, shape = TRUE, colour = "darkblue") +
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233 geom_point(size = 1, color = "red") +
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234 xlab(paste("PC1", summary(tdf_pca)$importance[2, 1] * 100, "%")) +
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235 ylab(paste("PC2", summary(tdf_pca)$importance[2, 2] * 100, "%")) +
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236 ggtitle("PCA")
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237 ggsave(file = opt$pca_out, device = "pdf")
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238 }
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239 }
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240
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241 # at this stage, we select numeric columns and round theirs values to 8 decimals for cleaner output
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242 is_num <- sapply(res, is.numeric)
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243 res[is_num] <- lapply(res[is_num], round, 8)
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244
0
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245 write.table(
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246 cbind(Features = rownames(res), res),
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247 opt$out,
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248 col.names = opt$colnames,
4
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249 row.names = FALSE,
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250 quote = FALSE,
0
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251 sep = "\t"
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252 )