build_matrices

*This script will build single-cell pair-wise distance (PWD) matrices, proximity frequency maps, and N-matrices from each Trace_ file in the buildsPWDmatrix folder. *

Invoke

Inside the folder with your input data, run:

pyhim -C build_matrix

Inputs

Name shape	Quantity	Mandatory	Description
parameters.json	1	Yes	Parameter file.

Outputs

Name shape	Quantity	Description

Relevant options

Parameters to run this script will be read from the buildsPWDmatrix field of parameters.json.

"colormaps":{"PWD_KDE":"terrain","PWD_median":"terrain","contact":"coolwarm","Nmatrix":"Blues"},

Output images:

• _PWDhistograms.png

• _Nmatrix.png

• HiMmatrix.png

• _PWDmatrixMedian.png

• _PWDmatrixKDE.png

example uses fiducial mask

method	contact matrices	PWD matrix
2D - mask
3D - mask
KDtree 3D
Nmatrices	Masking	KDTREE