diff R/heatmaply.R @ 3:e42d30da7a74 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/R/heatmaply.R	Thu May 30 11:52:25 2024 +0000
@@ -0,0 +1,49 @@
+#!/usr/bin/R
+
+library(heatmaply)
+library("optparse")
+
+option_list = list(
+  make_option(c("-f", "--file"), type="character", default=NULL,
+              help="dataset file name", metavar="character"),
+  make_option(c("-o", "--out"), type="character", default="out.txt",
+              help="output file name [default= %default]", metavar="character"),
+  make_option(c("-r", "--rowmetadata"), type="character", default=NULL,
+              help="metadata for rows", metavar="character"),
+  make_option(c("-c", "--colmetadata"), type="character", default=NULL,
+              help="metadata for cols", metavar="character")
+);
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if (is.null(opt$file)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (input file).\n", call.=FALSE)
+}
+
+if (is.null(opt$out)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (out file).\n", call.=FALSE)
+}
+
+mydata <- read.table(opt$file, header=TRUE,sep="\t",row.names="Gene")
+#colmetadata <- read.table(opt$colmetadata,sep="\t")
+#rowmetadata <- read.table(opt$rowmetadata,sep="\t")
+
+#metadata_tooltips <- read.table(paste(opt$file,"metadata_tooltips.txt",sep = "."),sep="\t")
+
+#mat <- metadata_tooltips
+#mat <- mydata
+#mat[] <- paste("\nCountry: ", rowmetadata[, 2], "\nContinent: ", rowmetadata[, 3], "\nCOG: ", colmetadata)
+
+heatmaply(mydata,file = "heatmaply.html")
+
+
+#heatmaply(
+#t(mydata), file = opt$out,
+#custom_hovertext = mat,
+#col_side_colors = colmetadata[, 3],
+#row_side_colors = rowmetadata[, 2:4],
+#scale_fill_gradient_fun = ggplot2::scale_fill_gradient2(
+#            low = "white" , mid="#E7E4EA", high = "#471777", limits = c(0, 1))
+#)