Run CellphoneDB analysis

Usage

RunCellphoneDB(
  srt,
  group.by,
  species = c("Homo_sapiens", "Mus_musculus"),
  assay = NULL,
  layer = "data",
  counts_data = c("hgnc_symbol", "ensembl", "gene_name"),
  method = c("statistical_analysis", "analysis", "degs_analysis"),
  cpdb_file_path = NULL,
  convert_to_human = TRUE,
  gene_id_from_IDtype = "symbol",
  microenvs = NULL,
  active_tfs = NULL,
  degs = NULL,
  score_interactions = TRUE,
  threshold = 0.1,
  pvalue = 0.05,
  iterations = 1000,
  cores = 1,
  separator = "|",
  debug = FALSE,
  debug_seed = 42,
  result_precision = 3,
  subsampling = FALSE,
  subsampling_log = FALSE,
  subsampling_num_pc = 100,
  subsampling_num_cells = 1000,
  output_path = NULL,
  output_suffix = NULL,
  keep_output = FALSE,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
group.by: Name of one or more meta.data columns to group (color) cells by.
species: Species of the input data. CellphoneDB is human-centric; when a non-human species is supplied and convert_to_human = TRUE, gene symbols will be converted to human ortholog symbols before running the analysis.
assay: Assay to use.
layer: Layer to use as CellphoneDB input. Default is "data" because CellphoneDB generally expects normalized expression.
counts_data: Gene identifier type used by CellphoneDB. One of "hgnc_symbol", "ensembl", or "gene_name".
method: CellphoneDB analysis mode. One of "statistical_analysis", "analysis", or "degs_analysis".
cpdb_file_path: Path to cellphonedb.zip. If NULL, the wrapper will try common locations and download it automatically when not found.
convert_to_human: Whether to convert non-human gene symbols to human ortholog symbols before running CellphoneDB.
gene_id_from_IDtype: Input gene identifier type passed to GeneConvert when convert_to_human = TRUE.
microenvs: Optional CellphoneDB microenvironment specification. Can be a data.frame or a file path.
active_tfs: Optional CellphoneDB active TF specification. Can be a data.frame or a file path.
degs: Optional DEG table for method = "degs_analysis". Can be a data.frame or a file path.
score_interactions: Whether to compute CellphoneDB interaction scores.
threshold: Minimum fraction of cells expressing a gene for the gene to be considered.
pvalue: P-value threshold used by CellphoneDB.
iterations: Number of permutations for statistical analysis.
cores: Number of cores used by CellphoneDB.
separator: Separator used by CellphoneDB for sender/receiver pair columns.
debug: Whether to ask CellphoneDB to save intermediate debug tables.
debug_seed: Random seed used by CellphoneDB.
result_precision: Result precision used by CellphoneDB.
subsampling: Whether to enable CellphoneDB subsampling.
subsampling_log: Whether to log-transform during CellphoneDB subsampling.
subsampling_num_pc: Number of PCs used during CellphoneDB subsampling.
subsampling_num_cells: Number of cells retained during CellphoneDB subsampling.
output_path: Optional directory to keep CellphoneDB output files.
output_suffix: Optional output suffix passed to CellphoneDB.
keep_output: Whether to keep temporary output files when output_path is not supplied.
verbose: Whether to print the message. Default is TRUE.

Value

A Seurat object with results stored in srt@tools[["CellphoneDB"]].