scPlotRegion

scPlotRegion plots signal from individual cells in a given genomic region as a heatmap (in the style of a trackplot), togather with the summary profiles (pseudobulk signal) on top.

usage: 
scPlotRegion -i INPUT_binned.h5ad --region CHROM:START-END -o OUTPUT_PREFIX

Input/Output options

--input, -i

sincei-generated input file in .h5ad format.

--outFilePrefix, -o

Prefix for output file names.

Plot Options

--region, -r

Genomic region in CHROM:START-END format

--mode, -m

Possible choices: sum, mean

How to aggregate signal for plotting the summary profiles (pseudobulk) on top. (default: 'sum')

--signalMin

Minimum value for pseudobulk track plot (default: minimum signal in the region)

--signalMax

Maximum value for pseudobulk summary profile (default: maximum signal in the region)

--hmapMin

Minimum value for single-cell heatmap signal (default: minimum signal in the region)

--hmapMax

Maximum value for single-cell heatmap signal (default: maximum signal in the region)

--summaryPlotColor

Color for the pseudobulk summary profile plot (default: 'red')

--colorMap

Colormap for heatmap. Must be a valid matplotlib colormap entry (default: 'Reds')

--figsize

Figure size in inches (<width>, <height>; (default: (14, 8)))

--dpi

DPI for output PNG (default: 300)

--outFileFormat

Possible choices: png, pdf, svg, eps, plotly

image format type. If given, this option overrides the image format inferred from the suffix of the outFilePrefix

Other options

--verbose, -v

Set to see processing messages.

-V, --version

Print the program version and exit.