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1 #!/usr/bin/Rscript
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2
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3 #usage, options and doc goes here
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4 argspec <- c("plot_distribution.r - plots distribution of the value in the list or the matrix. Assumes the first line and the first column are annotations.
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5 Usage:
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6 plot_distribution.r input_matrix.tab output_file.pdf
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7 Example:
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8 Rscript plot_distribution.r input_matrix.tab output_file.pdf
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9 Options:
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10 input file name
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11 output file name")
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12
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13 read_matrix <- function(in_file){
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14 header <- strsplit(readLines(con=in_file, n=1), "\t")[[1]]
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15 cl.cols<- 1:length(header) > 1
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16 data_matrix.df <- read.delim(in_file, header=TRUE, row.names=NULL, stringsAsFactors=FALSE, na.strings="NA", check.names=FALSE)
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17 data_matrix <- as.matrix(data_matrix.df[,cl.cols])
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18 rownames(data_matrix) <- data_matrix.df[,1]
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19 return(data_matrix)
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20 }
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21
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22 main <- function(argv) {
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23 in_file <- argv[1]
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24 out_file <- argv[2]
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25 sink('/dev/null')
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26
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27 input_data <- read_matrix(in_file)
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28 input_data.df <- as.data.frame(input_data)
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29 input_data.lst <- as.list(input_data.df)
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30 input_data.unlst <- unlist(input_data.lst)
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31 input_data.nona <- input_data.unlst[!is.na(input_data.unlst)]
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32
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33 pdf(out_file, bg="white")
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34 par(mfrow=c(1,1))
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35 hist(input_data.nona, col="lightblue", labels=TRUE, main="Histogram", xlab="")
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36 plot(density(input_data.nona), type="l", col="blue", main="Density")
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37 dev.off()
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38 }
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39 main(commandArgs(TRUE)) |
