Calculate cell-cell communication mediated by secreted proteins from spatial transcriptomics data.
Usage
SecAct.CCC.scST(
SpaCET_obj,
cellType_meta,
scale.factor = 1000,
radius = 20,
ratio_cutoff = 0.2,
padj_cutoff = 0.01,
coreNo = 6
)Arguments
- SpaCET_obj
A SpaCET object.
- cellType_meta
Column name in meta data that includes cell-type annotations.
- scale.factor
Sets the scale factor for spot-level normalization.
- radius
Radius cut off (unit: um).
- ratio_cutoff
Ratio cut off.
- padj_cutoff
Adjusted p value cut off.
- coreNo
Core number in parallel computation.