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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,95 +1,101 @@ | ||
| options(show.error.messages = FALSE, | ||
| error = function() { | ||
| cat(geterrmessage(), file = stderr()) | ||
| q("no", 1, FALSE) | ||
| } | ||
| options( | ||
| show.error.messages = FALSE, | ||
| error = function() { | ||
| cat(geterrmessage(), file = stderr()) | ||
| q("no", 1, FALSE) | ||
| } | ||
| ) | ||
| loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | ||
| warnings() | ||
| library(optparse) | ||
|
|
||
| # Arguments | ||
| option_list <- list( | ||
| make_option( | ||
| "--data", | ||
| default = NA, | ||
| type = "character", | ||
| help = "Input file that contains values to transform. Must be tabular separated, | ||
| make_option( | ||
| "--data", | ||
| default = NA, | ||
| type = "character", | ||
| help = "Input file that contains values to transform. Must be tabular separated, | ||
| with columns and row names, variables in rows, observations in columns [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--center", | ||
| default = TRUE, | ||
| type = "logical", | ||
| help = "center data to the mean [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--scale", | ||
| default = TRUE, | ||
| type = "logical", | ||
| help = "scale data to standard deviation [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--factor", | ||
| default = "", | ||
| type = "character", | ||
| help = "A two-column observations|factor_levels table, to group observations to be transformed by levels [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--output", | ||
| default = "res.tab", | ||
| type = "character", | ||
| help = "Table of transformed values [default : '%default' ]" | ||
| ) | ||
| ), | ||
| make_option( | ||
| "--center", | ||
| default = TRUE, | ||
| type = "logical", | ||
| help = "center data to the mean [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--scale", | ||
| default = TRUE, | ||
| type = "logical", | ||
| help = "scale data to standard deviation [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--factor", | ||
| default = "", | ||
| type = "character", | ||
| help = "A two-column observations|factor_levels table, to group observations to be transformed by levels [default : '%default' ]" | ||
| ), | ||
| make_option( | ||
| "--output", | ||
| default = "res.tab", | ||
| type = "character", | ||
| help = "Table of transformed values [default : '%default' ]" | ||
| ) | ||
| ) | ||
|
|
||
| transform <- function(df, center = TRUE, scale = TRUE) { | ||
| transfo <- scale(t(df), | ||
| center = center, | ||
| scale = scale | ||
| ) | ||
| return(as.data.frame(t(transfo))) | ||
| transfo <- scale(t(df), | ||
| center = center, | ||
| scale = scale | ||
| ) | ||
| return(as.data.frame(t(transfo))) | ||
| } | ||
|
|
||
| opt <- parse_args(OptionParser(option_list = option_list), | ||
| args = commandArgs(trailingOnly = TRUE)) | ||
| args = commandArgs(trailingOnly = TRUE) | ||
| ) | ||
|
|
||
| data <- read.delim( | ||
| opt$data, | ||
| check.names = FALSE, | ||
| header = TRUE, | ||
| row.names = 1, | ||
| sep = "\t" | ||
| opt$data, | ||
| check.names = FALSE, | ||
| header = TRUE, | ||
| row.names = 1, | ||
| sep = "\t" | ||
| ) | ||
|
|
||
| if (opt$factor != "") { | ||
| data_factor <- read.delim( | ||
| opt$factor, | ||
| check.names = FALSE, | ||
| header = TRUE, | ||
| sep = "\t", | ||
| stringsAsFactors = TRUE | ||
| ) | ||
| colnames(data_factor) <- c("cellid", "level") | ||
| data_transformed <- data.frame(row.names = rownames(data)) | ||
| for (group in levels(data_factor$level)) { | ||
| subcells <- as.data.frame(subset(data_factor, level == group, select = cellid)) | ||
| subdata <- as.data.frame(subset(data, select = as.vector(subcells$cellid))) | ||
| subdata_transformed <- transform(subdata, center = as.logical(opt$center), | ||
| scale = as.logical(opt$scale)) | ||
| data_transformed <- cbind(data_transformed, subdata_transformed) | ||
| } | ||
| data_factor <- read.delim( | ||
| opt$factor, | ||
| check.names = FALSE, | ||
| header = TRUE, | ||
| sep = "\t", | ||
| stringsAsFactors = TRUE | ||
| ) | ||
| colnames(data_factor) <- c("cellid", "level") | ||
| data_transformed <- data.frame(row.names = rownames(data)) | ||
| for (group in levels(data_factor$level)) { | ||
| subcells <- as.data.frame(subset(data_factor, level == group, select = cellid)) | ||
| subdata <- as.data.frame(subset(data, select = as.vector(subcells$cellid))) | ||
| subdata_transformed <- transform(subdata, | ||
| center = as.logical(opt$center), | ||
| scale = as.logical(opt$scale) | ||
| ) | ||
| data_transformed <- cbind(data_transformed, subdata_transformed) | ||
| } | ||
| } else { | ||
| data_transformed <- transform(data, center = as.logical(opt$center), | ||
| scale = as.logical(opt$scale)) | ||
| data_transformed <- transform(data, | ||
| center = as.logical(opt$center), | ||
| scale = as.logical(opt$scale) | ||
| ) | ||
| } | ||
|
|
||
|
|
||
| write.table( | ||
| cbind(gene = rownames(data_transformed), data_transformed), | ||
| opt$output, | ||
| col.names = TRUE, | ||
| row.names = FALSE, | ||
| quote = FALSE, | ||
| sep = "\t" | ||
| cbind(gene = rownames(data_transformed), data_transformed), | ||
| opt$output, | ||
| col.names = TRUE, | ||
| row.names = FALSE, | ||
| quote = FALSE, | ||
| sep = "\t" | ||
| ) |