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 |