# start snippet aggregate basic
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg
# end snippet aggregate basic

# start snippet aggregate plot
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p architecture/aggregate/fanc_example_100kb.agg.png \
               -m architecture/aggregate/fanc_example_100kb.agg.txt
# end snippet aggregate plot
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_100kb.agg.png \
               -m architecture/aggregate/fanc_example_100kb.agg.txt

# start snippet aggregate oe
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p architecture/aggregate/fanc_example_100kb_oe.agg.png \
               -m architecture/aggregate/fanc_example_100kb_oe.agg.txt \
               -e -l
# end snippet aggregate oe
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_100kb_oe.agg.png \
               -m architecture/aggregate/fanc_example_100kb_oe.agg.txt \
               -e -l

# start snippet aggregate expand
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p architecture/aggregate/fanc_example_100kb_oe_large.agg.png \
               -m architecture/aggregate/fanc_example_100kb_oe_large.agg.txt \
               -e -l -r 1.0
# end snippet aggregate expand
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_100kb_oe_large.agg.png \
               -m architecture/aggregate/fanc_example_100kb_oe_large.agg.txt \
               -e -l -r 1.0

# start snippet aggregate rescale
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p architecture/aggregate/fanc_example_100kb_oe_large_res.png \
               -m architecture/aggregate/fanc_example_100kb_oe_large.agg.txt \
               -e -r 1.0 --rescale --vmax 0.045
# end snippet aggregate rescale
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_100kb_oe_large_res.png \
               -m architecture/aggregate/fanc_example_100kb_oe_large.agg.txt \
               -e -r 1.0 --rescale --vmax 0.045

# start snippet aggregate tads
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg \
               -p architecture/aggregate/fanc_example_100kb_oe_large.agg.png \
               -m architecture/aggregate/fanc_example_100kb_oe_large.agg.txt \
               --tads
# end snippet aggregate tads

# start snippet aggregate fixed
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/fanc_example_100kb.insulation_boundaries_score0.7_1mb.bed \
               architecture/aggregate/fanc_example_100kb_boundaries.agg \
               -w 5mb -p architecture/aggregate/fanc_example_100kb_boundaries.agg.png \
               -m architecture/aggregate/fanc_example_100kb_boundaries.agg.txt \
               --vmin 0 --vmax 0.03
# end snippet aggregate fixed
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/fanc_example_100kb.insulation_boundaries_score0.7_1mb.bed \
               architecture/aggregate/fanc_example_100kb_boundaries.agg \
               -w 5mb -p ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_100kb_boundaries.agg.png \
               -m architecture/aggregate/fanc_example_100kb_boundaries.agg.txt \
               --vmin 0 --vmax 0.03

# start snippet aggregate oefixed
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/fanc_example_100kb.insulation_boundaries_score0.7_1mb.bed \
               architecture/aggregate/fanc_example_100kb_boundaries_oe.agg \
               -w 5mb -p architecture/aggregate/fanc_example_100kb_boundaries_oe.agg.png \
               -m architecture/aggregate/fanc_example_100kb_boundaries_oe.agg.txt \
               -e -l
# end snippet aggregate oefixed
fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/fanc_example_100kb.insulation_boundaries_score0.7_1mb.bed \
               architecture/aggregate/fanc_example_100kb_boundaries_oe.agg \
               -w 5mb -p ../docsrc/fanc-executable/fanc-analyse-hic/images/fanc_example_100kb_boundaries_oe.agg.png \
               -m architecture/aggregate/fanc_example_100kb_boundaries_oe.agg.txt \
               -e -l

# start snippet aggregate loops
fanc aggregate architecture/loops/rao2014.chr11_77400000_78600000.hic \
               architecture/loops/rao2014.chr11_77400000_78600000.loops_no_singlets.bedpe \
               architecture/loops/rao2014.chr11_77400000_78600000.loops_no_singlets.agg \
               -p architecture/aggregate/rao2014.chr11_77400000_78600000.loops_no_singlets.agg.png \
               --loops
# end snippet aggregate loops
fanc aggregate architecture/loops/rao2014.chr11_77400000_78600000.hic \
               architecture/loops/rao2014.chr11_77400000_78600000.loops_no_singlets.bedpe \
               architecture/loops/rao2014.chr11_77400000_78600000.loops_no_singlets.agg \
               -p ../docsrc/fanc-executable/fanc-analyse-hic/images/rao2014.chr11_77400000_78600000.loops_no_singlets.agg.png \
               --loops