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