diff PanExplorer_workflow/R/heatmap_ani.R @ 1:032f6b3806a3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/R/heatmap_ani.R	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,73 @@
+#!/usr/local/R-4.1.2/bin/R
+
+library(RColorBrewer)
+library(dendextend)
+library("optparse")
+
+#args = commandArgs(trailingOnly=TRUE)
+
+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")
+);
+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)
+}
+
+#svglite(opt$out,width = 31, height = 28)
+pdf(opt$out,width = 31,height = 28)
+
+mydata <- read.table(opt$file, header=TRUE,sep="\t", row.names="Genomes")
+
+iris <- mydata
+
+#dend_r <- iris %>% dist(method = "man") %>% hclust(method = "ward.D") %>% as.dendrogram %>% ladderize
+dend_r <- iris %>% dist(method = "man") %>% hclust(method = "com") %>% as.dendrogram %>% ladderize
+
+#dend_c <- t(iris) %>% dist(method = "man") %>% hclust(method = "com") %>% as.dendrogram %>% ladderize
+dend_c <- t(iris) %>% dist(method = "man") %>% hclust(method = "ward.D") %>% as.dendrogram %>% ladderize
+
+
+#write(hc2Newick(dend_c),file='hclust.newick')
+Colors=c("yellow","red")
+Colors=colorRampPalette(Colors)(100)
+mat <- as.matrix(t(iris-1))
+out <- gplots::heatmap.2(mat,
+          main = "",
+          scale="none",
+          #srtCol=NULL,
+          Rowv = dend_r,
+          Colv = dend_r,
+          #key = FALSE,
+          margins =c(20,20),
+          col=Colors,
+          trace="row", hline = NA, tracecol = NA
+         )
+
+write.table(
+  data.frame(gene = rownames(mat)[out$rowInd]),
+  paste(opt$out, "rows.csv", sep="."),
+  row.names = FALSE,
+  quote = FALSE,
+  sep = ',')
+
+write.table(
+  data.frame(gene = colnames(mat)[out$colInd]),
+  paste(opt$out, "cols.csv", sep="."),
+  row.names = FALSE,
+  quote = FALSE,
+  sep = ',')
+
+dev.off()
+