deeptools_plotcorrelation

#!/bin/bash

if [[ -z $1 ]]; then
	echo "Usage: "
	echo -e "\t\$1: The file which record the bigwig files and their labels. "
	echo -e "\t    An example file (separated by tab) is as follows:"
	echo -e "\t\t    /PATH/TO/bigwig1 sample1"
	echo -e "\t\t    /PATH/TO/bigwig2 sample2"
	echo -e "\t\t    ..."
	echo -e "\t\$2: The output_dir."
	echo -e "\t\$3: The bin size, default 200."
	echo -e "\t\$4: The thread, default 20."
	echo -e "\t\$5: The png figure width, default 20."
	echo -e "\t\$6: The png figure height, default 15."

	exit 100
fi

input=$1
output=$2
binsize=$3
thread=$4
width=$5
height=$6

# default setting
if true; then
	deeptools_plotcorrelation_R=~/Program/Custom_tools/deeptools_plotcorrelation.R

	if [[ -z ${binsize} ]]; then
		binsize=200
	fi
	if [[ -z ${thread} ]]; then
		thread=20
	fi
	if [[ -z ${width} ]]; then
		width=20
	fi
	if [[ -z ${height} ]]; then
		height=15
	fi
fi

# create the directory
mkdir -p ${output}/{1.raw_data,2.correlation_data,3.correlation}

# get parameters
if true; then
	bw_files=$(cut -f1 ${input} | xargs)
	labels=$(cut -f2 ${input} | xargs)
	npz=${output}/1.raw_data/multiBigwigSummary_bs200.npz
	tab=${output}/1.raw_data/multiBigwigSummary_bs200.tab
	cor_mat=${output}/2.correlation_data/pearson_correlation_bs200.tab
	cor_pic=${output}/3.correlation/pearson_correlation_bs200.pdf
	custom_cor_pic=${output}/3.correlation/pearson_correlation_bs200.png
fi

# run the program
if true; then
	# get matrix
	multiBigwigSummary bins --bwfiles ${bw_files} \
		--outFileName ${npz} \
		--outRawCounts ${tab} \
		--labels ${labels} \
		--binSize ${binsize} --numberOfProcessors ${thread}
	
	# correlation calculation
	plotCorrelation --corData ${npz} \
		--plotFile ${cor_pic} \
		--outFileCorMatrix ${cor_mat} \
		--corMethod pearson --whatToPlot heatmap \
		--skipZeros --colorMap bwr

	# replot correlation
	Rscript ${deeptools_plotcorrelation_R} -i ${cor_mat} -o ${custom_cor_pic} -w ${width} -H ${height} -u 1 -l -1
fi