scHicPlotClusterProfiles¶
usage: scHicPlotClusterProfiles --matrix scool scHi-C matrix --clusters
cluster file
[--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
[--maximalDistance MAXIMALDISTANCE]
[--distanceShortRange DISTANCESHORTRANGE]
[--distanceLongRange DISTANCELONGRANGE]
[--orderBy {svl,orderByFile}]
[--fontsize FONTSIZE] [--rotationX ROTATIONX]
[--ticks | --legend]
[--outFileName OUTFILENAME] [--dpi DPI]
[--colorMap COLORMAP] [--threads THREADS]
[--help] [--version]
Named Arguments¶
- --ticks
Plot the cluster names as ticks. Use legend if they overlap.
Default: False
- --legend
Plot the cluster names as legend. Might be helpful if the ticks overlap.
Default: False
Required arguments¶
- --matrix, -m
The single cell Hi-C interaction matrices to investigate for QC. Needs to be in scool format
- --clusters, -c
Text file which contains per matrix the associated cluster.
Optional arguments¶
- --chromosomes
List of to be plotted chromosomes
- --maximalDistance, -md
Maximal distance in bases to consider for ratio computation.
Default: 50000000
- --distanceShortRange, -ds
Distance which should be considered as lower distance for svl ordering. Values from distances smaller this value are not considered. Default 2MB.
Default: 2000000
- --distanceLongRange, -dl
Distance which should be considered as upper distance for svl ordering. Values from distances greater this value are not considered. Default 12MB.
Default: 12000000
- --orderBy, -ob
Possible choices: svl, orderByFile
Algorithm to cluster the Hi-C matrices
Default: “svl”
- --fontsize
Fontsize in the plot for x and y axis.
Default: 10
- --rotationX
Rotation in degrees for the labels of x axis.
Default: 0
- --outFileName, -o
File name to save the resulting cluster profile.
Default: “clusters_profile.png”
- --dpi, -d
The dpi of the plot.
Default: 300
- --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”
- --threads, -t
Number of threads. Using the python multiprocessing module.
Default: 4
- --version
show program’s version number and exit