dec_cci: Decomposing cell-cell communications for spatial...
In ZJUFanLab/SpaTalk: Infer Cell-Cell Communication for Spatial Transcriptomics

dec_cci

R Documentation

Decomposing cell-cell communications for spatial transciptomics data

Description

Identify the cell-cell communications for single-cell or spot-based spatial transciptomics data with proximal ligand-receptor-target interactions.

Usage

dec_cci(
  object,
  celltype_sender,
  celltype_receiver,
  n_neighbor = 10,
  min_pairs = 5,
  min_pairs_ratio = 0,
  per_num = 1000,
  pvalue = 0.05,
  co_exp_ratio = 0.1,
  if_doParallel = T,
  use_n_cores = NULL
)

Arguments

`object`	SpaTalk object after `find_lr_path`.
`celltype_sender`	Name of celltype_sender.
`celltype_receiver`	Name of celltype_receiver.
`n_neighbor`	Number of neighbor cells to select as the proximal cell-cell pair. Default is `10`.
`min_pairs`	Min proximal cell-cell pairs between for sending and receiving cell types. Default is `5`.
`min_pairs_ratio`	Min proximal cell-cell pairs ratio between for sending and receiving cell types. Default is `0`.
`per_num`	Number of repeat times for permutation test. Default is `1000`.
`pvalue`	Include the significantly proximal LR pairs with this cutoff of p value from permutation test. Default is `0.05`.
`co_exp_ratio`	Min cell ratio in receiving cells with co-expressed source and target genes for predicting the downstream pathway activity.
`if_doParallel`	Use doParallel. Default is TRUE.
`use_n_cores`	Number of CPU cores to use. Default is all cores - 2.