--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/center_scale.R	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,101 @@
+options( show.error.messages=F,
+       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+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,
+            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' ]"
+  )
+)
+
+transform <- function(df, center=TRUE, scale=TRUE) {
+    transfo <- scale(
+        t(df),
+        center=center,
+        scale=center
+        )
+    return(as.data.frame(t(transfo)))
+}
+
+opt = parse_args(OptionParser(option_list = option_list),
+                 args = commandArgs(trailingOnly = TRUE))
+
+data = read.table(
+    opt$data,
+    check.names = FALSE,
+    header = TRUE,
+    row.names = 1,
+    sep = '\t'
+)
+
+if (opt$factor != '') {
+    data.factor = read.table(
+        opt$factor,
+        check.names = FALSE,
+        header = TRUE,
+        sep = '\t'
+        )
+    colnames(data.factor) <- c("cellid", "level")
+    data.transformed <- data.frame(row.names=rownames(data), stringsAsFactors=FALSE)
+    for (group in levels(data.factor$level)){
+        subcells <- as.data.frame(subset(data.factor, level==group, select=cellid))
+        subdata <- as.data.frame(subset(data, select=subcells$cellid))
+        subdata.transformed <- transform(subdata, center=opt$center, scale=opt$scale)
+        data.transformed <- cbind(data.transformed, subdata.transformed)
+    }
+} else {
+    data.transformed <- transform(data, center=opt$center, scale=opt$scale)
+}
+
+
+write.table(
+  cbind(gene=rownames(data.transformed), data.transformed),
+  opt$output,
+  col.names = TRUE,
+  row.names = FALSE,
+  quote = F,
+  sep = "\t"
+)
+
+
+
+
+
+
+
+
+
+
+
+