Plot_Trace.R

#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)

source("PolyGraphFunc.R")

file <- args[1]
qfile <- args[2]
phenoname <- args[3]
graphscript <- args[4]
output_boxplot <- args[5]
output_phenograph <- args[6]
output_phenograph_qfile <- args[7]
minbranch <- args[8]

# Load admixture graph
source(graphscript)

if( file != "NA"){
    # Load table
    table <- read.table(file,header=TRUE)
    # Remove burn-in
    trace <- table[seq(10,dim(table)[1]-1,1),]

    # Make pheno-graph from trace output
    pdf(output_phenograph,width = 8, height = 8)
    minsel <- -0.3
    maxsel <- 0.3
    MakeGraphPlot(file,edgevalues,"r",phenoname,minsel,maxsel,minbranch)
    dev.off()
}
    
# Make pheno-graph from qfile output
pdf(output_phenograph_qfile,width = 8, height = 8)
minsel <- -10
maxsel <- 10
MakeGraphPlotQfile(qfile,edgevalues,"r",phenoname,minsel,maxsel,minbranch)
dev.off()
 
# Make boxplot
if( file != "NA"){
    SNPs <- max(sapply(colnames(table),function(x){as.numeric(paste(unlist(strsplit(gsub("[^0-9]", "", x),"")),collapse=""))}),na.rm=TRUE)
    titleboxplot <- paste("Posterior distributions of alpha parameters: ",phenoname," (num. SNPs: ",SNPs,")",sep="")
    pdf(output_boxplot,width=15,height=5)
    finalboxplot <- AlphaBoxPlot(trace,titleboxplot,FALSE,0)
    grid.arrange(finalboxplot,ncol=1,nrow=1)
    dev.off()
}