scHicPlotConsensusMatrices

usage: scHicPlotConsensusMatrices --matrix scool scHi-C matrix
                                  [--outFileName OUTFILENAME] [--dpi DPI]
                                  [--threads THREADS]
                                  [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                                  [--region REGION] [--colorMap COLORMAP]
                                  [--fontsize FONTSIZE] [--no_header]
                                  [--log1p] [--individual_scale] [--help]
                                  [--version]

Required arguments

--matrix, -m

The consensus matrix created by scHicConsensusMatrices

Optional arguments

--outFileName, -o

File name to save the resulting cluster profile.

Default: “consensus_matrices.png”

--dpi, -d

The dpi of the plot.

Default: 300

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--chromosomes, -c

List of to be plotted chromosomes

--region, -r

Region to be plotted for each consensus matrix. Mutual exclusion with the usage of –chromosomes parameter

--colorMap

Color map to use for the heatmap. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html

Default: “RdYlBu_r”

--fontsize

Fontsize in the plot for x and y axis.

Default: 10

--no_header

Do not plot a header.

Default: True

--log1p

Apply log1p operation to plot the matrices.

Default: False

--individual_scale

Use an individual value range for all cluster consensus matrices. If not set, the same scale is applied to all.

Default: True

--version

show program’s version number and exit