plot_compare2matrices

Reliability status: development

Comparison of proximity matrices. Plots either the ratio or the difference between two HiM matrices. It also plots both matrices together, with one in the upper triangle, and the other in the lower triangle.

usage: plot_compare2matrices [-h] [-O OUTPUTFOLDER] [-T1 INPUT1] [-T2 INPUT2]
                             [-U UNIQUEBARCODES] [--fontsize FONTSIZE]
                             [--axisLabel] [--axisTicks] [--ratio]
                             [--plottingFileExtension PLOTTINGFILEEXTENSION]
                             [--normalize NORMALIZE] [--pixelSize PIXELSIZE]
                             [--matrix_norm_mode MATRIX_NORM_MODE]
                             [--dist_calc_mode DIST_CALC_MODE]
                             [--proximity_threshold PROXIMITY_THRESHOLD]
                             [--cMax CMAX]
                             [--scalingParameter SCALINGPARAMETER]
                             [--shuffle SHUFFLE] [--cMin CMIN] [--cmap CMAP]

Named Arguments

-O, --outputFolder

Folder for outputs

-T1, --input1

Filename of single-cell PWD matrices in Numpy

-T2, --input2

Filename of single-cell PWD matrices in Numpy

-U, --uniqueBarcodes

csv file with list of unique barcodes

--fontsize

Size of fonts to be used in matrix

--axisLabel

Use if you want a label in x and y

Default: False

--axisTicks

Use if you want axes ticks

Default: False

--ratio

Does ratio between matrices. Default: difference

Default: False

--plottingFileExtension

By default: svg. Other options: pdf, png

--normalize

Matrix normalization factor: maximum, none, single value (normalize 2nd matrix by), bin pair e.g. 1,2

--pixelSize

pixelSize in microns

--matrix_norm_mode

Matrix normalization mode. Can be n_cells (default) or nonNANs

--dist_calc_mode

Mode used to calculate the mean distance. Can be either ‘median’, ‘KDE’ or ‘proximity’. Default: median

--proximity_threshold

proximity threshold in um

--cMax

Colormap max scale. Default: automatic

--scalingParameter

Scaling parameter. Default: 1

--shuffle

Provide shuffle vector: 0,1,2,3… of the same size or smaller than the original matrix. No spaces! comma-separated!

--cMin

Colormap min cscale. Default: 0

--cmap

Colormap. Default: coolwarm