SpatCCI: cellphoneDB for spot-population

In YeehanXiao/STREAM: STREAM: Spatial Transcriptomics data Analyses and Modeling

cellphoneDB for spot-population

Description

cellphoneDB for spot-population

cellphonedb_merge

Usage

SpatCellphoneDB(
  object,
  outputFolder = NULL,
  numCores = 4,
  Geneformat = "hgnc_symbol",
  cellphonedbPath = NULL,
  method = "kmeans",
  ...
)

cellphonedb_merge(interaction)

Arguments

object	A giotto object
outputFolder	Output folder to save results.
numCores	The number of cores to use, default as 4.
Geneformat	Format of gene name in count matrix, one of "ensembl_gene", "gene_symbol".
cellphonedbPath	Path to launch cellphoneDB.
method	Spatial clustering method to annotate spots population, either "kmeans" or "HMRF".
...	other arguments
interaction	A list out of cellphoneDB calculation.

YeehanXiao/STREAM documentation built on Aug. 13, 2022, 6:43 p.m.