plot_n_him_matrices

Reliability status: development

plots N Hi-M matrices in a subplot

Plots several (N) HiM matrices in the same plot, using N datasets specified in folders2Load.json.

It also plots a submatrix representing the difference in contact probability for a subset of barcodes compared to a particular dataset. The subset of barcodes and the reference dataset are defined in folders2Load.json by the options barcodes2plot and plotSegment_anchor, respectively.

usage: plot_n_him_matrices [-h] [-F ROOTFOLDER] [-O OUTPUTFOLDER]
                           [-P PARAMETERS] [-A LABEL] [-W ACTION]
                           [--fontsize FONTSIZE] [--axisLabel] [--axisTicks]
                           [--barcodes] [--scalingParameter SCALINGPARAMETER]
                           [--plottingFileExtension PLOTTINGFILEEXTENSION]
                           [--shuffle SHUFFLE] [--scalogram] [--type TYPE]
                           [--pixelSize PIXELSIZE] [--cAxis CAXIS] [--ratio]
                           [--normalizeMatrix]

Named Arguments

-F, --rootFolder

Folder with dataset

-O, --outputFolder

Folder for outputs

-P, --parameters

Provide name of parameter files. folders_to_load.json assumed as default

-A, --label

Add name of label (e.g. doc)

-W, --action

Select: [all], [labeled] or [unlabeled] cells plotted

--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

--barcodes

Use if you want barcode images to be displayed

Default: False

--scalingParameter

Scaling parameter of colormap

--plottingFileExtension

By default: svg. Other options: pdf, png

--shuffle

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

--scalogram

Use if you want scalogram image to be displayed

Default: False

--type

Provide one of the following: PWD, contact, iPWD

--pixelSize

Provide pixelSize in um

--cAxis

absolute cAxis value for colormap

--ratio

Does ratio between matrices. Default: difference

Default: False

--normalizeMatrix

Normalizes matrices by maximum. Default: True

Default: False