Compare Kernel density distributions

[Duy Dinh]

!/bin/bash

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R script to display kernel distribution of groups of MAP values obtained by different runs

@author: Duy Dinh

@date: 22 March 2012

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library(sm)

result directory

path = "/home/duy/collection/TRECGenomics-2004/participants"

get file names from directory

fileFilter="*.txt"

full names

files = list.files(path, full.names=TRUE, pattern=fileFilter)

short names

names = list.files(path, pattern=fileFilter)

outputImage=TRUE

outputImage=FALSE

output image

outputImg = paste(path, "output", sep="/")
outputImg = paste(outputImg, "png", sep=".")

start graphics drawing

if (outputImage == TRUE){
#postscript(file=outputImg, horizontal=FALSE, width=15, height=8)
png(filename=outputImg)
}

xAxisLabel = "MAP"
yAxisLabel = "Densité"
xAxisRange = c(0.0, 1.0)
yAxisRange = c(0.0, 3.0)
n=length(files)

if (n > 0){

# distribute plots
par(mfrow=c(1,n))

for (i in 1 : n){

# read MAP values from a csv file (header in the first line)
table = read.table(files[i], header=TRUE)

# Build run names 
runNames = c("pllsgen4a2", "uwmtDg04tn", "pllsgen4a1", "PDTNsmp4", "Spe-MH-OM+PRF")
run <- factor( rep(runNames, each=length(table$SpeMHOM))) # number of queries

# MAP per run data frame
mpre <- data.frame(run, map=c(table$pllsgen4a2,table$uwmtDg04tn, table$pllsgen4a1, table$PDTNsmp4, table$SpeMHOM))

# graphical parameters

lineColors = c("red","blue", "cyan", "black","chartreuse")
pChars=c(20:24)
lineTypes=c(10:length(mpre$run))

# plot a group of kernel density curves 
sm.density.compare(mpre$map, # vector of data
        mpre$run, # vector of group labels            
        xlab=xAxisLabel, ylab=yAxisLabel,
        xlim=xAxisRange, ylim=yAxisRange,
        col=lineColors, pch=pChars, lty=lineTypes,
        title=names[i]
)

# Add a legend for which line types, colors represent appropriately the corresponding runs
#legend("topright", levels(mpre$run), lty=lineTypes, col=lineColors, pch=pChars)    
legend("topright", levels(mpre$run), lty=lineTypes, col=lineColors)

}
}

if (outputImage){
dev.off()
}

[Duy Dinh]

QueryID pllsgen4a2 uwmtDg04tn pllsgen4a1 PDTNsmp4 SpeMHOM
1 0.4 0.3 0.5 0.2 0.6
2 0.2 0.4 0.34 0.32 0.55
3 0.5 0.46 0.54 0.42 0.75
4 0.25 0.60 0.43 0.22 0.35
5 0.45 0.30 0.42 0.22 0.15