Mercurial > repos > artbio > ez_histograms

annotate ez_histograms.R @ 1:fbedb212982d draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
author artbio
date Thu, 08 Feb 2024 02:15:11 +0000
parents bdf40b0924cb
children d375c9df9c34
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bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
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diff changeset
1 library(ggplot2)
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
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2 library(reshape2)
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
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3 library(dplyr)
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
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4 library(scales)
1
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
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5 library(psych)
0
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
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6 library(optparse)
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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7
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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8 options(show.error.messages = FALSE,
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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9 error = function() {
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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10 cat(geterrmessage(), file = stderr())
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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11 q("no", 1, FALSE)
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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12 }
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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13 )
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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14
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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16 warnings()
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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17
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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18 option_list <- list(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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19 make_option(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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20 c("-f", "--file"),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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21 default = NA,
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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22 type = "character",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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23 help = "Input file that contains count values to transform"
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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24 ),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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25 make_option(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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26 c("-d", "--profile"),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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27 default = "count",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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28 type = "character",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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29 help = "Whether y-axis shows absolute counts or density: 'count' or 'density' [default : '%default' ]"
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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30 ),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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31 make_option(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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32 "--xscale",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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33 default = "cartesian",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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34 type = "character",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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35 help = "Whether x-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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36 ),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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37 make_option(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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38 "--yscale",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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39 default = "cartesian",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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40 type = "character",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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41 help = "Whether y-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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42 ),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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43 make_option(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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44 c("-p", "--pdf"),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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45 default = "histograms.pdf",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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46 type = "character",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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47 help = "Output pdf file name [default : '%default' ]"
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48 ),
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49 make_option(
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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50 c("-s", "--summary"),
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51 default = "summary.tsv",
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52 type = "character",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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53 help = "statistics summary file name [default : '%default' ]"
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54 )
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55 )
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56
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57 opt <- parse_args(OptionParser(option_list = option_list),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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58 args = commandArgs(trailingOnly = TRUE))
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59
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60 plot_histograms <- function(mdata, profile = "count", xscale = "cartesian", yscale = "cartesian", bins = 30) {
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61 if (profile == "count") {
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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62 # count histogram
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63 p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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64 geom_histogram(bins = bins) + theme(legend.position = "none")
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65 if (xscale == "cartesian") {
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66 if (yscale == "log2") {
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67 p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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68 } else {
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69 if (yscale == "log10") {
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70 p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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71 }
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72 }
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73 }
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74 if (xscale == "log2") {
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75 p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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76 if (yscale == "log2") {
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77 p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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78 } else {
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79 if (yscale == "log10") {
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80 p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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81 }
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82 }
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83 }
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84 if (xscale == "log10") {
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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85 p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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86 if (yscale == "log2") {
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87 p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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88 } else {
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89 if (yscale == "log10") {
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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90 p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
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91 }
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92 }
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93 }
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94 }
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95
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96 if (profile == "density") {
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97 # density histogram
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98 p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +
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99 geom_density() + theme(legend.position = "none")
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100 if (xscale == "log2") {
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101 p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
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102 }
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103 if (xscale == "log10") {
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104 p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
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105 }
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106 }
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107 return(p)
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108 }
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109
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110 test_header <- function(file) {
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111 data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)
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112 if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {
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113 return(TRUE)
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114 } else {
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115 return(FALSE)
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116 }
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117 }
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118
1
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119 ##### prepare input data
0
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120
1
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121 data <- read.delim(file = opt$file, header = test_header(opt$file))
0
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122 data <- data %>% select(where(is.numeric)) # remove non numeric columns
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123 mdata <- melt(data)
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124
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125 ##### main
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126
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127 # determine optimal number of bins (Sturges’ Rule)
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128 bins <- ceiling(log2(nrow(data)) + 1)
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129 # plot
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130 p <- plot_histograms(mdata, profile = opt$profile, xscale = opt$xscale, bins = bins, yscale = opt$yscale)
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131
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132 # determine optimal width for the graph
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133 width <- length(data)
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134 width <- case_when(
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135 width == 1 ~ 14 / 3,
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136 width == 2 ~ (2 / 3) * 14,
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137 TRUE ~ 14
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138 )
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139 # determine optimal height for the graph
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140 height <- length(data)
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141 height <- case_when(
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142 height <= 3 ~ 3,
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143 height <= 6 ~ 6,
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144 TRUE ~ (floor(height / 3) + 1) * 3
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145 )
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146 # determine optimal number of col for the graph
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147 ncol <- length(data)
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148 ncol <- case_when(
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149 ncol == 1 ~ 1,
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150 ncol == 2 ~ 2,
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151 TRUE ~ 3
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152 )
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153 pdf(opt$pdf, width = width, height = height)
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154 print(p + facet_wrap(~variable, ncol = ncol, scales = "free"))
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155 dev.off()
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156
1
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157 # Summary statistics with psych package
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158 summary_df <- describe(x = data, skew = FALSE, ranges = FALSE, quant = c(.25, .50, .75))
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159 summary_df <- cbind(var_names = rownames(summary_df), summary_df)
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160 colnames(summary_df)[2] <- "var_num"
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161 summary_df <- summary_df[, -6]
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162 summary_df[, 4:8] <- format(summary_df[, 4:8], scientific = TRUE)
0
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163 write.table(summary_df, file = opt$summary, sep = "\t", quote = FALSE, row.names = FALSE)