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lib/Genome/Model/Tools/Music/Plot/MutationRelation.pm.R  view on Meta::CPAN

# Fetch command line arguments
args = commandArgs();
input_matrix = as.character(args[4]);
genes_to_plot = as.character(args[5]);
output_pdf = as.character(args[6]);
preserveGeneOrder = as.numeric(as.character(args[7]));

sort.data.frame <- function( x, by ) {
    if(by[[1]] != "~")
        stop("Argument 'by' must be a one-sided formula.")

    ## Make the formula into character and remove spaces
    formc <- as.character(by[2])
    formc <- gsub(" ", "", formc)
    ## If the first character is not + or -, add +
    if(!is.element(substring(formc, 1, 1), c("+", "-")))
        formc <- paste("+", formc, sep = "")

    ## Extract the variables from the formula
    vars <- unlist(strsplit(formc, "[\\+\\-]"))
    vars <- vars[vars != ""] # Remove any extra "" terms

    ## Build a list of arguments to pass to "order" function
    calllist <- list()
    pos <- 1 # Position of + or -
    for(i in 1:length(vars)){
        varsign <- substring(formc, pos, pos)
        pos <- pos + 1 + nchar(vars[i])
        if(is.factor(x[, vars[i]])){
        if(varsign == "-") {
            calllist[[i]] <- -rank(x[, vars[i]])
        } else {
            calllist[[i]] <- rank(x[, vars[i]])
        }
        } else {
        if(varsign == "-") {
            calllist[[i]] <- -x[, vars[i]]
        } else {
            calllist[[i]] <- x[,vars[i]]
        }
        }
    }
    return( x[do.call( "order", calllist ), ] )
}

plotMutRel <- function( infile, genes, outfile, preserveGeneOrder=FALSE) {

    ##------------------
    a = read.table(infile,row.names=1,header=T)
    gene_list = unlist(strsplit(genes, split=","))
    print(genes)
    df=a[,gene_list]

    numSamp=length(df[,1])
    numGenes=length(df)

    if(numGenes < 1){
        return("Error: genes to plot not found in matrix")
    }

    ##adjustments to plot and text sizes for different numbers of samples
    samptext=0.3
    genetext=0.75
    pdfwidth=numSamp/10
    offset=2

    if(numSamp < 50){
        samptext=0.3
        #genetext=0.85
        pdfwidth=numSamp/5
        offset=1.25
    }
    if(numSamp < 35){
        samptext=0.4
    }
    if(pdfwidth < 3) { pdfwidth = 3 }
#    if(numSamp >=100) { genetext=1.1 }
#    if(numSamp >=200) { genetext=1.1 }