Mercurial > repos > artbio > gsc_center_scale

annotate center_scale.R @ 3:b7daf62bde65 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
author artbio
date Thu, 07 Nov 2024 18:54:17 +0000
parents 163befe5f05b
children
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3
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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1 options(
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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2 show.error.messages = FALSE,
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3 error = function() {
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4 cat(geterrmessage(), file = stderr())
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5 q("no", 1, FALSE)
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6 }
2
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7 )
0
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 warnings()
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10 library(optparse)
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11
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12 # Arguments
2
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13 option_list <- list(
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14 make_option(
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15 "--data",
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16 default = NA,
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17 type = "character",
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18 help = "Input file that contains values to transform. Must be tabular separated,
0
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19 with columns and row names, variables in rows, observations in columns [default : '%default' ]"
3
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20 ),
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21 make_option(
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22 "--center",
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23 default = TRUE,
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24 type = "logical",
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25 help = "center data to the mean [default : '%default' ]"
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26 ),
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27 make_option(
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28 "--scale",
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29 default = TRUE,
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30 type = "logical",
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31 help = "scale data to standard deviation [default : '%default' ]"
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32 ),
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33 make_option(
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34 "--factor",
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35 default = "",
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36 type = "character",
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37 help = "A two-column observations|factor_levels table, to group observations to be transformed by levels [default : '%default' ]"
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38 ),
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39 make_option(
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40 "--output",
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41 default = "res.tab",
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42 type = "character",
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43 help = "Table of transformed values [default : '%default' ]"
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44 )
0
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45 )
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46
2
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47 transform <- function(df, center = TRUE, scale = TRUE) {
3
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48 transfo <- scale(t(df),
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49 center = center,
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50 scale = scale
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51 )
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52 return(as.data.frame(t(transfo)))
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53 }
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54
2
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55 opt <- parse_args(OptionParser(option_list = option_list),
3
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56 args = commandArgs(trailingOnly = TRUE)
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57 )
0
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58
2
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59 data <- read.delim(
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60 opt$data,
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61 check.names = FALSE,
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62 header = TRUE,
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63 row.names = 1,
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64 sep = "\t"
0
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65 )
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66
2
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67 if (opt$factor != "") {
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68 data_factor <- read.delim(
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69 opt$factor,
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70 check.names = FALSE,
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71 header = TRUE,
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72 sep = "\t",
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73 stringsAsFactors = TRUE
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74 )
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75 colnames(data_factor) <- c("cellid", "level")
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76 data_transformed <- data.frame(row.names = rownames(data))
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77 for (group in levels(data_factor$level)) {
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78 subcells <- as.data.frame(subset(data_factor, level == group, select = cellid))
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79 subdata <- as.data.frame(subset(data, select = as.vector(subcells$cellid)))
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80 subdata_transformed <- transform(subdata,
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81 center = as.logical(opt$center),
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82 scale = as.logical(opt$scale)
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83 )
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84 data_transformed <- cbind(data_transformed, subdata_transformed)
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85 }
0
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86 } else {
3
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87 data_transformed <- transform(data,
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88 center = as.logical(opt$center),
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89 scale = as.logical(opt$scale)
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90 )
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bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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91 }
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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94 write.table(
3
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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95 cbind(gene = rownames(data_transformed), data_transformed),
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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96 opt$output,
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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97 col.names = TRUE,
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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98 row.names = FALSE,
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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99 quote = FALSE,
b7daf62bde65 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale commit 44d7e1048de3a58983e0559581264147090fefb0
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100 sep = "\t"
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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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101 )