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annotate center_scale.R @ 2:163befe5f05b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 41ba5435a8ad12c1fe0703a9ce44b759003f3f73
author artbio
date Sun, 15 Oct 2023 16:16:16 +0000
parents a96cc346819c
children b7daf62bde65
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163befe5f05b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 41ba5435a8ad12c1fe0703a9ce44b759003f3f73
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1 options(show.error.messages = FALSE,
163befe5f05b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 41ba5435a8ad12c1fe0703a9ce44b759003f3f73
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2 error = function() {
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3 cat(geterrmessage(), file = stderr())
163befe5f05b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 41ba5435a8ad12c1fe0703a9ce44b759003f3f73
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4 q("no", 1, FALSE)
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5 }
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6 )
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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8 warnings()
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9 library(optparse)
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11 # Arguments
2
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12 option_list <- list(
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13 make_option(
2
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14 "--data",
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15 default = NA,
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16 type = "character",
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17 help = "Input file that contains values to transform. Must be tabular separated,
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18 with columns and row names, variables in rows, observations in columns [default : '%default' ]"
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19 ),
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20 make_option(
2
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21 "--center",
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22 default = TRUE,
2
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23 type = "logical",
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24 help = "center data to the mean [default : '%default' ]"
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25 ),
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26 make_option(
2
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27 "--scale",
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28 default = TRUE,
2
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29 type = "logical",
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30 help = "scale data to standard deviation [default : '%default' ]"
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31 ),
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32 make_option(
2
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33 "--factor",
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34 default = "",
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35 type = "character",
0
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36 help = "A two-column observations|factor_levels table, to group observations to be transformed by levels [default : '%default' ]"
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37 ),
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38 make_option(
2
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39 "--output",
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40 default = "res.tab",
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41 type = "character",
0
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42 help = "Table of transformed values [default : '%default' ]"
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43 )
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44 )
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45
2
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46 transform <- function(df, center = TRUE, scale = TRUE) {
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47 transfo <- scale(t(df),
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48 center = center,
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49 scale = scale
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50 )
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51 return(as.data.frame(t(transfo)))
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52 }
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53
2
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54 opt <- parse_args(OptionParser(option_list = option_list),
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55 args = commandArgs(trailingOnly = TRUE))
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56
2
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57 data <- read.delim(
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58 opt$data,
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59 check.names = FALSE,
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60 header = TRUE,
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61 row.names = 1,
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62 sep = "\t"
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63 )
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64
2
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65 if (opt$factor != "") {
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66 data_factor <- read.delim(
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67 opt$factor,
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68 check.names = FALSE,
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69 header = TRUE,
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70 sep = "\t",
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71 stringsAsFactors = TRUE
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72 )
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73 colnames(data_factor) <- c("cellid", "level")
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74 data_transformed <- data.frame(row.names = rownames(data))
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75 for (group in levels(data_factor$level)) {
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76 subcells <- as.data.frame(subset(data_factor, level == group, select = cellid))
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77 subdata <- as.data.frame(subset(data, select = as.vector(subcells$cellid)))
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78 subdata_transformed <- transform(subdata, center = as.logical(opt$center),
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79 scale = as.logical(opt$scale))
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80 data_transformed <- cbind(data_transformed, subdata_transformed)
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81 }
0
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82 } else {
2
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83 data_transformed <- transform(data, center = as.logical(opt$center),
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84 scale = as.logical(opt$scale))
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85 }
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86
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87
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88 write.table(
2
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89 cbind(gene = rownames(data_transformed), data_transformed),
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bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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90 opt$output,
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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91 col.names = TRUE,
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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92 row.names = FALSE,
2
163befe5f05b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 41ba5435a8ad12c1fe0703a9ce44b759003f3f73
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93 quote = FALSE,
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bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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94 sep = "\t"
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
artbio
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95 )