cellphonedb Algorithm

Purpose

Use cellphonedb for cell communication analysis

Usage

SDAS CCI cellphonedb -i st.h5ad --label_key anno_spotlight -o outdir \
--method statistical \
--counts_data hgnc_symbol \
--species human

Input Parameter Description

Parameter	Required	Default	Description
-i / --input	Yes		h5ad file, must contain raw expression matrix
-o / --output	Yes		Output folder
--label_key	Yes		Column name used to distinguish cell types in cell communication analysis
--method	No	statistical	Analysis method, options: simple, statistical, degs
--layer	No		Name of the layer in h5ad containing the raw expression matrix
--counts_data	No	hgnc_symbol	Type of var.index in the adata: 'ensembl', 'gene_name', 'hgnc_symbol'
--threshold	No	0.1	Percentage of cells expressing the specific ligand/receptor [0.0 - 1.0]
--species	No	human	SDAS built-in cellphonedb human database, version v5.0.0; when --cellphonedb_database is specified, this parameter is ignored
--cellphonedb_database	No		Path to user-defined cellphonedb database file
--pvalue	No	0.05	Significance threshold (filtering interactions with p ≤ pvalue), parameter for method=statistical
--subsampling	No		Whether to subsample, parameter for method=statistical
--subsampling_num_cells	No		Number of cells to subsample to [1/3 of cells], effective when using --subsampling, parameter for method=statistical
--microenvs_file_path	No		Path to microenvironment file (two columns: cell type, spatial microenvironment)
--active_tfs_file_path	No		Path to active transcription factor file (two columns: cell type, TF)
--degs_file_path	No		Path to differentially expressed gene file (two columns: cell type, DEG), required for method=degs
--n_cpus	No	8	Number of threads
--seed	No	42	Random seed

Output Results Display

Result File	Description
simple_analysis_means_result_<input_name>.txt statistical_analysis_means_result_<input_name>.txt degs_analysis_means_result_<input_name>.txt	Matrix of average expression for all ligand-receptor pairs. Each row is a ligand-receptor pair, each column is a cell type combination, value is average expression
simple_analysis_deconvoluted_<input_name>.txt statistical_analysis_deconvoluted_<input_name>.txt degs_analysis_deconvoluted_<input_name>.txt	Average expression of each cell type, used to show the expression of each cell type
simple_analysis_deconvoluted_percents_<input_name>.txt statistical_analysis_deconvoluted_percents_<input_name>.txt degs_analysis_deconvoluted_percents_<input_name>.txt	Expression ratio of each cell type, reflecting the percentage of each ligand-receptor pair in different cell types
simple_analysis_interaction_scores_<input_name>.txt statistical_analysis_interaction_scores_<input_name>.txt degs_analysis_interaction_scores_<input_name>.txt	Interaction strength score between cell types, the larger the value, the stronger the ligand-receptor interaction
statistical_analysis_significant_means_<input_name>.txt degs_analysis_significant_means_<input_name>.txt	Average expression of significant interactions
statistical_analysis_pvalues_<input_name>.txt	Matrix of significance p-values for all ligand-receptor pairs under statistical method
cellphonedb_heatmap_<input_name>.png/pdf	Heatmap of significant interactions, showing the strength of significant ligand-receptor interactions between all cell clusters, color depth reflects interaction strength, output when method=statistical and degs

• Heatmap of significant interactions output by cellphonedb: cellphonedb_heatmap_<input_name>.png/pdf shows the heatmap of significant ligand-receptor interactions between all cell clusters, color depth reflects interaction strength. Both axes are cell clusters, color depth indicates interaction strength, the deeper the color, the stronger the interaction. Quickly compare the activity of communication between different cell clusters.