plot_3way_coloc

Reliability status: development

Replot 3-way co-localization matrices from .npy files.

It visualizes the frequency of co-localization between barcodes with reference to an anchor barcode, highlighting the anchor’s position with perpendicular lines on the heatmap.

usage: plot_3way_coloc [-h] [--input [INPUT ...]] [--pipe] [--vmin VMIN]
                       [--vmax VMAX] [--cmap CMAP]
                       [--label_map_file LABEL_MAP_FILE]
                       [--plot_format PLOT_FORMAT]

Named Arguments

--input

List of input .npy matrix files.

Default: []

--pipe

Read filenames from stdin

Default: False

--vmin

Minimum color scale value

--vmax

Maximum color scale value

--cmap

Matplotlib colormap (default: RdBu)

Default: 'RdBu'

--label_map_file

Text file with barcode numbers per row

--plot_format

Available options: svg, pdf, png

Default: 'png'

Basic Usage

plot_3way_coloc --input path/to/matrix1.npy path/to/matrix2.npy