Mercurial > repos > artbio > cpm_tpm_rpk

annotate cpm_tpm_rpk.R @ 7:f00c1c34565e draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
author artbio
date Wed, 03 Jul 2024 14:39:26 +0000
parents bcff1eb6fdb5
children
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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) {
7
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
artbio
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2 system("Rscript cpm_tpm_rpk.R -h", intern = FALSE)
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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3 q("no")
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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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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
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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,
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f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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9 error = function() {
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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10 cat(geterrmessage(), file = stderr())
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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11 q("no", 1, FALSE)
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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12 }
4
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)
4
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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563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
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20 library(ggfortify)
1
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21
0
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22
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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23 #Arguments
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24 option_list <- list(
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25 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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26 c("-d", "--data"),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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27 default = NA,
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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28 type = "character",
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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29 help = "Input file that contains count values to transform"
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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30 ),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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31 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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32 c("-t", "--type"),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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33 default = "cpm",
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34 type = "character",
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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35 help = "Transformation type, either cpm, tpm, rpkm or none[default : '%default' ]"
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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36 ),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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37 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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38 c("-s", "--sep"),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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39 default = "\t",
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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40 type = "character",
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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41 help = "File separator [default : '%default' ]"
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42 ),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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43 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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44 c("-c", "--colnames"),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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45 default = TRUE,
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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46 type = "logical",
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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47 help = "Consider first line as header ? [default : '%default' ]"
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48 ),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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49 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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50 c("-f", "--gene"),
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51 default = NA,
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52 type = "character",
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53 help = "Two column of gene length file"
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54 ),
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55 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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56 c("-a", "--gene_sep"),
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57 default = "\t",
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58 type = "character",
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59 help = "Gene length file separator [default : '%default' ]"
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60 ),
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61 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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62 c("-b", "--gene_header"),
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63 default = TRUE,
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64 type = "logical",
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65 help = "Consider first line of gene length as header ? [default : '%default' ]"
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66 ),
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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67 make_option(
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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68 c("-l", "--log"),
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69 default = FALSE,
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70 type = "logical",
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71 help = "Should be log transformed as well ? (log2(data +1)) [default : '%default' ]"
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72 ),
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73 make_option(
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74 c("-o", "--out"),
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75 default = "res.tab",
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76 type = "character",
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77 help = "Output name [default : '%default' ]"
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78 ),
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79 make_option(
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80 "--visu",
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81 default = FALSE,
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82 type = "logical",
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83 help = "performs T-SNE [default : '%default' ]"
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84 ),
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85 make_option(
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86 "--tsne_labels",
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87 default = FALSE,
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88 type = "logical",
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89 help = "add labels to t-SNE plot [default : '%default' ]"
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90 ),
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91 make_option(
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92 "--seed",
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93 default = 42,
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94 type = "integer",
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95 help = "Seed value for reproducibility [default : '%default' ]"
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96 ),
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97 make_option(
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98 "--perp",
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99 default = 5.0,
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100 type = "numeric",
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101 help = "perplexity [default : '%default' ]"
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102 ),
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103 make_option(
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104 "--theta",
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105 default = 1.0,
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106 type = "numeric",
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107 help = "theta [default : '%default' ]"
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108 ),
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109 make_option(
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110 c("-D", "--tsne_out"),
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111 default = "tsne.pdf",
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112 type = "character",
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113 help = "T-SNE pdf [default : '%default' ]"
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114 ),
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115 make_option(
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116 "--pca_out",
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117 default = "pca.pdf",
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118 type = "character",
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119 help = "PCA pdf [default : '%default' ]"
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120 )
2
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121
0
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122 )
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123
4
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124 opt <- parse_args(OptionParser(option_list = option_list),
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125 args = commandArgs(trailingOnly = TRUE))
0
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126
4
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127 if (opt$data == "" && !(opt$help)) {
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128 stop("At least one argument must be supplied (count data).\n",
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129 call. = FALSE)
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130 } else if ((opt$type == "tpm" || opt$type == "rpkm") && opt$gene == "") {
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131 stop("At least two arguments must be supplied (count data and gene length file).\n",
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132 call. = FALSE)
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133 } else if (opt$type != "tpm" && opt$type != "rpkm" && opt$type != "cpm" && opt$type != "none") {
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134 stop("Wrong transformation requested (--type option) must be : cpm, tpm or rpkm.\n",
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135 call. = FALSE)
0
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136 }
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137
4
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138 if (opt$sep == "tab") {
7
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139 opt$sep <- "\t"
4
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140 }
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141 if (opt$gene_sep == "tab") {
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142 opt$gene_sep <- "\t"
4
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143 }
0
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144
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145 cpm <- function(count) {
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146 (count / colSums(count)) * 1000000
0
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147 }
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148
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149
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150 rpk <- function(count, length) {
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151 count / (length / 1000)
0
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152 }
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153
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154 tpm <- function(count, length) {
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155 rpk <- rpk(count, length)
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156 per_million_factor <- colSums(rpk) / 1000000
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157 tpm <- rpk / per_million_factor
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158 return(tpm)
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159 }
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160
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161 rpkm <- function(count, length) {
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162 rpk <- rpk(count, length)
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163 per_million_factor <- colSums(as.data.frame(count)) / 1000000
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164 rpkm <- rpk / per_million_factor
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165 return(rpkm)
0
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166 }
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167
4
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168 #### running code ####
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169
5
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170 data <- read.delim(
7
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171 opt$data,
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172 check.names = FALSE,
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173 header = opt$colnames,
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174 row.names = 1,
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175 sep = opt$sep
0
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176 )
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177
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178 if (opt$type == "tpm" || opt$type == "rpkm") {
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179 gene_length <- as.data.frame(
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180 read.delim(
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181 opt$gene,
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182 header = opt$gene_header,
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183 row.names = 1,
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184 sep = opt$gene_sep
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185 )
0
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186 )
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187 gene_length <- as.data.frame(gene_length[match(rownames(data), rownames(gene_length)), ], rownames(data))
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188 }
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189
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190
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191 if (opt$type == "cpm") {
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192 res <- cpm(data)
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193 }
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194 if (opt$type == "tpm") {
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195 res <- as.data.frame(apply(data, 2, tpm, length = gene_length), row.names = rownames(data))
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196 }
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197 if (opt$type == "rpkm") {
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198 res <- as.data.frame(apply(data, 2, rpkm, length = gene_length), row.names = rownames(data))
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199 }
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200 if (opt$type == "none") {
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201 res <- data
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202 }
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203 colnames(res) <- colnames(data)
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204
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205 if (opt$log == TRUE) {
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206 res <- log2(res + 1)
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207 }
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208
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209 if (opt$visu == TRUE) {
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210 df <- res
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211 # filter and transpose df for tsne and pca
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212 df <- df[rowSums(df) != 0, ] # remove lines without information (with only 0 counts)
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213 tdf <- t(df)
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214 # make tsne and plot results
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215 set.seed(opt$seed) ## Sets seed for reproducibility
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216 tsne_out <- Rtsne(tdf, perplexity = opt$perp, theta = opt$theta)
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217 embedding <- as.data.frame(tsne_out$Y)
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218 embedding$Class <- as.factor(sub("Class_", "", rownames(tdf)))
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219 gg_legend <- theme(legend.position = "none")
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220 ggplot(embedding, aes(x = V1, y = V2)) +
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221 geom_point(size = 1, color = "red") +
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222 gg_legend +
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223 xlab("") +
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224 ylab("") +
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225 ggtitle("t-SNE") +
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226 if (opt$tsne_labels == TRUE) {
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227 geom_text(aes(label = Class), hjust = -0.2, vjust = -0.5, size = 2.5, color = "darkblue")
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228 }
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229 ggsave(file = opt$tsne_out, device = "pdf")
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230 # make PCA and plot result with ggfortify (autoplot)
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231 tdf_pca <- prcomp(tdf, center = TRUE, scale. = TRUE)
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232 if (opt$tsne_labels == TRUE) {
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233 autoplot(tdf_pca, shape = FALSE, label = TRUE, label.size = 2.5, label.vjust = 1.2,
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234 label.hjust = 1.2,
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235 colour = "darkblue") +
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236 geom_point(size = 1, color = "red") +
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237 xlab(paste("PC1", summary(tdf_pca)$importance[2, 1] * 100, "%")) +
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238 ylab(paste("PC2", summary(tdf_pca)$importance[2, 2] * 100, "%")) +
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239 ggtitle("PCA")
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240 ggsave(file = opt$pca_out, device = "pdf")
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241 } else {
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242 autoplot(tdf_pca, shape = TRUE, colour = "darkblue") +
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243 geom_point(size = 1, color = "red") +
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244 xlab(paste("PC1", summary(tdf_pca)$importance[2, 1] * 100, "%")) +
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245 ylab(paste("PC2", summary(tdf_pca)$importance[2, 2] * 100, "%")) +
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246 ggtitle("PCA")
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247 ggsave(file = opt$pca_out, device = "pdf")
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248 }
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249 }
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250
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251 # at this stage, we select numeric columns and round theirs values to 8 decimals for cleaner output
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252 is_num <- sapply(res, is.numeric)
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253 res[is_num] <- lapply(res[is_num], round, 8)
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254
0
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255 write.table(
7
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256 cbind(Features = rownames(res), res),
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257 opt$out,
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258 col.names = opt$colnames,
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259 row.names = FALSE,
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260 quote = FALSE,
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
artbio
parents: 5
diff changeset
261 sep = "\t"
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
262 )