annotate R/heatmap.R @ 13:152d7c43478b draft default tip

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#!/usr/local/R-4.1.2/bin/R


library(dendextend)
library("optparse")
library(reshape2)
library(ape)


#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="Gene")

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

#dend_c


distance_matrix = t(iris) %>% dist(method = "man")
h = distance_matrix %>% hclust(method = "ward.D")

tree = as.phylo(h)


dend_c = h %>% as.dendrogram


write.tree(tree, file=paste(opt$out, "distance_matrix.hclust.newick", sep="."))

dist_df <- melt(as.matrix(distance_matrix), varnames = c("row", "col"))
write.table(
  dist_df,
  paste(opt$out, "distance_matrix.txt", sep=".")
)

mat <- as.matrix(t(iris-1))
out <- gplots::heatmap.2(mat,
          main = "",
          scale="none",
          srtCol=NULL,
          Rowv = dend_c,
          #Colv = dend_r,
          key = FALSE,
          margins =c(20,20),
          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()