comparison heatmap_viz.R @ 1:b8a5139cf5b9 draft

planemo upload commit 5dd4a8814abf4a735409189a4c7cfe3ffd207c62-dirty

0:edbb84a94a36

  #}
  return(uto)
}

get_cols <-function(input_cols) {
  input_cols <- gsub("c","",input_cols)
  if (grepl(":",input_cols)) {
    first_col=unlist(strsplit(input_cols,":"))[1]
    last_col=unlist(strsplit(input_cols,":"))[2]
    cols=first_col:last_col
  } else {

header=str2bool(args$header)
output <- rapply(strsplit(args$output,"\\."),c) #remove extension
output <- paste(output[1:length(output)-1],collapse=".")
output <- paste(output,args$type,sep=".")
cols = get_cols(args$cols)
rownames_col = as.integer(gsub("c","",args$row_names))
if (length(cols) <=1 ){
  stop("You need several colums to build a heatmap")
}
dist=args$dist
clust=args$clust

uto <- read_file(args$input,header)
uto <- clean_df(uto,cols,rownames_col)
uto <- uto[rowSums(is.na(uto)) != ncol(uto), ]  #remove emptylines

if (header) {
  col_names = names(data)
} else {
  col_names = cols
}

#building heatmap

1:b8a5139cf5b9

  #}
  return(uto)
}

get_cols <-function(input_cols) {
  input_cols <- gsub("c","",gsub("C","",gsub(" ","",input_cols)))
  if (grepl(":",input_cols)) {
    first_col=unlist(strsplit(input_cols,":"))[1]
    last_col=unlist(strsplit(input_cols,":"))[2]
    cols=first_col:last_col
  } else {

header=str2bool(args$header)
output <- rapply(strsplit(args$output,"\\."),c) #remove extension
output <- paste(output[1:length(output)-1],collapse=".")
output <- paste(output,args$type,sep=".")
cols = get_cols(args$cols)
rownames_col = as.integer(gsub("c","",gsub("C","",gsub(" ","",args$row_names))))
if (length(cols) <=1 ){
  stop("You need several colums to build a heatmap")
}
dist=args$dist
clust=args$clust

uto <- read_file(args$input,header)
uto <- clean_df(uto,cols,rownames_col)
uto <- uto[rowSums(is.na(uto)) != ncol(uto), ]  #remove emptylines

if (header) {
  col_names = names(uto)
} else {
  col_names = cols
}

#building heatmap