
# start snippet compartments basic
fanc compartments output/hic/binned/fanc_example_1mb.hic architecture/compartments/fanc_example_1mb.ab
# end snippet compartments basic

# start snippet compartments plot
fancplot -o architecture/compartments/fanc_example_1mb.ab.png chr18 \
     -p square architecture/compartments/fanc_example_1mb.ab \
     -vmin -0.75 -vmax 0.75 -c RdBu_r
# end snippet compartments plot

fancplot -o ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_1mb.ab.png chr18 \
     -p square architecture/compartments/fanc_example_1mb.ab \
     -vmin -0.75 -vmax 0.75 -c RdBu_r


# start snippet compartments ev
fanc compartments -v architecture/compartments/fanc_example_1mb.ev.txt \
                  output/hic/binned/fanc_example_1mb.hic \
                  architecture/compartments/fanc_example_1mb.ab
# end snippet compartments ev

# start snippet
fanc compartments -v architecture/compartments/fanc_example_1mb.ev.txt \
                  architecture/compartments/fanc_example_1mb.ab

# start snippet compartments pre
fanc compartments -v architecture/compartments/fanc_example_1mb.ev.txt \
                  architecture/compartments/fanc_example_1mb.ab
# end snippet compartments pre

# start snippet compartments evplot
fancplot -o architecture/compartments/fanc_example_1mb.ab_and_ev.png chr18 \
     -p square architecture/compartments/fanc_example_1mb.ab \
     -vmin -0.75 -vmax 0.75 -c RdBu_r \
     -p line architecture/compartments/fanc_example_1mb.ev.txt
# end snippet compartments evplot
fancplot -o ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_1mb.ab_and_ev.png chr18 \
     -p square architecture/compartments/fanc_example_1mb.ab \
     -vmin -0.75 -vmax 0.75 -c RdBu_r \
     -p line architecture/compartments/fanc_example_1mb.ev.txt

# start snippet compartments gc
fanc compartments -g hg19_chr18_19.fa -v architecture/compartments/fanc_example_1mb.ev_gc.txt \
                      architecture/compartments/fanc_example_1mb.ab
# end snippet compartments gc

# start snippet compartments domain
fanc compartments -d architecture/compartments/fanc_example_1mb.domains.bed \
                      architecture/compartments/fanc_example_1mb.ab
# end snippet compartments domain

# start snippet compartments gcdomain
fanc compartments -g hg19_chr18_19.fa \
                  -d architecture/compartments/fanc_example_1mb.domains_gc.bed \
                  architecture/compartments/fanc_example_1mb.ab
# end snippet compartments gcdomain


# start snippet compartments enrichment
fanc compartments -e architecture/compartments/fanc_example_1mb.ab_profile.png \
                  output/hic/binned/fanc_example_1mb.hic \
                  architecture/compartments/fanc_example_1mb.ab
# end snippet compartments enrichment
fanc compartments -e ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_1mb.ab_profile.png \
                  output/hic/binned/fanc_example_1mb.hic \
                  architecture/compartments/fanc_example_1mb.ab

# start snippet compartments gcenrichment
fanc compartments -g hg19_chr18_19.fa \
                  -e architecture/compartments/fanc_example_1mb.ab_profile.png \
                  output/hic/binned/fanc_example_1mb.hic \
                  architecture/compartments/fanc_example_1mb.ab
# end snippet compartments gcenrichment
fanc compartments -g hg19_chr18_19.fa \
                  -e ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_1mb.ab_profile.png \
                  output/hic/binned/fanc_example_1mb.hic \
                  architecture/compartments/fanc_example_1mb.ab

fanc compartments -g hg19_chr18_19.fa \
                  -e ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_1mb.ab_profile_sym.png \
                  -p 10 20 30 40 50 60 70 80 90 100 \
                  -s 0 \
                  output/hic/binned/fanc_example_1mb.hic \
                  architecture/compartments/fanc_example_1mb.ab