Generating plotsΒΆ

StripePy comes with a plot subcommand that can be used to generate various kinds of plots.

stripepy plot supports the following subcommands:

  • contact-map (cm): plot stripes and other features over the Hi-C matrix

  • pseudodistribution (pd): plot the pseudo-distribution over the given region of interest

  • stripe-hist (hist): generate and plot the histograms showing the distribution of the stripe heights and widths

stripepy cm takes as input a Hi-C matrix in .cool, .mcool, or .hic format, and optionally the .hdf5 file generated by stripepy call (this parameter is mandatory when highlighting stripes or stripe seeds).

stripepy pd and stripepy hist do not require the Hi-C matrix file, and require the .hdf5 file generated by stripepy call instead.

All three subcommands support specifying a region of interest through the --region option. When the commands are run without specifying the region of interest, stripepy cm and stripepy pd will generate plots for a random 2.5 Mbp region, while stripepy hist will generate histograms using data from the entire genome.

Example usage:

# Plot the pseudo-distribution over a region of interest
stripepy plot pd 4DNFI9GMP2J8.10000.hdf5 /tmp/pseudodistribution.png --region chr2:120100000-122100000

# Plot the histograms using genome-wide data
stripepy plot hist 4DNFI9GMP2J8.10000.hdf5 /tmp/stripe_hist_gw.png

# Plot the Hi-C matrix
stripepy plot cm 4DNFI9GMP2J8.mcool 10000 /tmp/matrix.png

# Plot the Hi-C matrix highlighting the stripe seeds
stripepy plot cm 4DNFI9GMP2J8.mcool 10000 /tmp/matrix_with_seeds.png --stripepy-hdf5 4DNFI9GMP2J8.10000.hdf5 --highlight-seeds

# Plot the Hi-C matrix highlighting the architectural stripes
stripepy plot cm 4DNFI9GMP2J8.mcool 10000 /tmp/matrix_with_stripes.png --stripepy-hdf5 4DNFI9GMP2J8.10000.hdf5 --highlight-stripes

Some example plots generated with stripepy plot can be found in file stripepy-plot-test-images.tar.xz from doi.org/10.5281/zenodo.14283921.