process_him_matrix

Reliability status: development

usage: process_him_matrix [-h] [-F ROOTFOLDER] [-P PARAMETERS] [-A LABEL]
                          [-W ACTION] [--matlab] [--saveMatrix]
                          [--getStructure] [--pixelSize PIXELSIZE]
                          [--HiMnormalization HIMNORMALIZATION] [--d3]

Named Arguments

-F, --rootFolder

Folder with images

-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

--matlab

Use to load matlab formatted data

Default: False

--saveMatrix

Use to load matlab formatted data

Default: False

--getStructure

Use to save ShEc3D PDB structure

Default: False

--pixelSize

pixelSize in um

--HiMnormalization

Normalization of contact matrix: nonNANs (default) or n_cells

--d3

Use to load 3D maps

Default: False

Output

sc_matrix_collated: 3D npy matrix. PWD matrix for single cells. Axes:0-1 barcodes, Axis:2, cellID unique_barcodes: npy array. list of unique barcodes SClabeledCollated: npy array. binary label indicating if cell is in pattern or not. Axis:0 cellID

Note

This script performs the post-processing of one or more datasets previously analysed with pyHiM, defined in the folders2Load.json file.

It performs the following operations:

  • Merges datasets from different experiments.

  • Calculates and plots ensemble pairwise distance (PWD) matrix.

  • Calculates and plots the inverse of the PWD matrix.

  • Calculates and plots contact probability matrix for each dataset.

  • Calculates and plots ensemble contact probability matrix.

  • Calculates and plots tensemble 3-way contact probability matrix for the set of anchors defined in the folders2Load.json file.

  • Optional: Reads MATLAB single-cell PWD matrices and performs all previous operations.