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