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Cell-cell communication from spatial data

Source: R/downstream.R
SecAct.CCC.scST.Rd

Calculate cell-cell communication mediated by secreted proteins from spatial transcriptomics data.

Usage

SecAct.CCC.scST(
  SpaCET_obj,
  cellType_meta,
  scale.factor = 1e+05,
  radius = 0.02,
  ratio_cutoff = 0.2,
  padj_cutoff = 0.01
)

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.

ratio_cutoff

Ratio cut off.

padj_cutoff

Adjusted p value cut off.

Value

A Seurat object.