Independent clustering

Clustering data using different methods and metrics (in matlab_scripts)

runAllClusters()

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Running Arboretum

Making orthology mapping for input of Arboretum

python python_scripts/makeOG.py data/human2mouse_1M.txt data/arboretum_ins/human2mouse.txt

Extracting sub-matrices using orthology mapping

for i in hESC hIMR90;
do
python python_scripts/makeSubMat.py data/human2mouse_1M.txt 0 data/1M_interaction/$i.txt data/sub_mats/$i.txt;
done
for i in mESC mCortex;
do
python python_scripts/makeSubMat.py data/human2mouse_1M.txt 1 data/1M_interaction/$i.txt data/sub_mats/$i.txt;
done

Making Eigenvectors using the Matlab script (in matlab_scripts)

getEigs()

Changing the region names

python python_scripts/convertNames.py data/human2mouse_1M.txt 0 data/arboretum_ins/eigs_oldname/hESC.10.eigs.txt data/arboretum_ins/hESC.eigs.txt hESC python python_scripts/convertNames.py data/human2mouse_1M.txt 0 data/arboretum_ins/eigs_oldname/hIMR90.10.eigs.txt data/arboretum_ins/hIMR90.eigs.txt hIMR90 python python_scripts/convertNames.py data/human2mouse_1M.txt 1 data/arboretum_ins/eigs_oldname/mESC.10.eigs.txt data/arboretum_ins/mESC.eigs.txt mESC python python_scripts/convertNames.py data/human2mouse_1M.txt 1 data/arboretum_ins/eigs_oldname/mCortex.10.eigs.txt data/arboretum_ins/mCortex.eigs.txt mCortex

Running Arboretum (from data/arboretum_ins/ directory)

../../arboretum2.0/arboretum -s specorder.txt -e human2mouse.txt -k 10 -t tree1.txt -c config.txt -r none -o arboretum_outs/ -m learn -b hESC -i uniform -p 0.8 -1 true -2 true -w true

Reordering the output cluster assignments

for h in hESC hIMR90;
do
python python_scripts/sortCluster.py data/human2mouse_1M.txt data/arboretum_ins/arboretum_outs/"$h"_speciesspecnames_clusterassign.txt data/arboretum_ins/arboretum_outs/"$h"_sorted.txt 0 $h;
done
for h in mESC mCortex;
do
python python_scripts/sortCluster.py data/human2mouse_1M.txt data/arboretum_ins/arboretum_outs/"$h"_speciesspecnames_clusterassign.txt data/arboretum_ins/arboretum_outs/"$h"_sorted.txt 1 $h;
done