CellCellColocation3D Pipeline¶
Calculate cell-cell colocation array by KL in 3D coordinate and then generate its MST.
Usage¶
python3 CellColocation.py
argument |
description |
|---|---|
-h, –help |
show this help message and exit |
-i |
in.h5ad |
-o |
prefix |
-b |
binsize (for each slice), default 50 (refer to 50um if 1 unit=1um). |
-m |
min cell number for a cell type, default 100. |
-f |
sample fraction, default 0.8. The bootstrap fraction. |
-l |
loop number, default 100. The number of iterations for bootstrap. |
-s |
spatial key in obsm, default ‘spatial’ |
-a |
annotation key in obs, default ‘annotation’ |
Please set -b based on your coordinate system !!!
Note: -b must be an integer
Reference¶
Wei, R., He, S., Bai, S. et al. Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnol 40, 1190–1199 (2022). https://doi.org/10.1038/s41587-022-01233-1