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3
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1 #!/usr/bin/R
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2
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3 library(heatmaply)
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4 library("optparse")
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5
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6 option_list = list(
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7 make_option(c("-f", "--file"), type="character", default=NULL,
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8 help="dataset file name", metavar="character"),
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9 make_option(c("-o", "--out"), type="character", default="out.txt",
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10 help="output file name [default= %default]", metavar="character"),
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11 make_option(c("-r", "--rowmetadata"), type="character", default=NULL,
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12 help="metadata for rows", metavar="character"),
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13 make_option(c("-c", "--colmetadata"), type="character", default=NULL,
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14 help="metadata for cols", metavar="character")
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15 );
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16 opt_parser = OptionParser(option_list=option_list);
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17 opt = parse_args(opt_parser);
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18
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19 if (is.null(opt$file)){
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20 print_help(opt_parser)
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21 stop("At least one argument must be supplied (input file).\n", call.=FALSE)
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22 }
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23
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24 if (is.null(opt$out)){
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25 print_help(opt_parser)
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26 stop("At least one argument must be supplied (out file).\n", call.=FALSE)
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27 }
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28
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29 mydata <- read.table(opt$file, header=TRUE,sep="\t",row.names="Gene")
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30 #colmetadata <- read.table(opt$colmetadata,sep="\t")
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31 #rowmetadata <- read.table(opt$rowmetadata,sep="\t")
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32
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33 #metadata_tooltips <- read.table(paste(opt$file,"metadata_tooltips.txt",sep = "."),sep="\t")
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34
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35 #mat <- metadata_tooltips
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36 #mat <- mydata
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37 #mat[] <- paste("\nCountry: ", rowmetadata[, 2], "\nContinent: ", rowmetadata[, 3], "\nCOG: ", colmetadata)
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38
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39 heatmaply(mydata,file = "heatmaply.html")
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40
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41
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42 #heatmaply(
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43 #t(mydata), file = opt$out,
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44 #custom_hovertext = mat,
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45 #col_side_colors = colmetadata[, 3],
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46 #row_side_colors = rowmetadata[, 2:4],
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47 #scale_fill_gradient_fun = ggplot2::scale_fill_gradient2(
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48 # low = "white" , mid="#E7E4EA", high = "#471777", limits = c(0, 1))
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49 #)
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