pyscenic Algorithm

Purpose

This module is based on pyscenic analysis of cell-gene expression matrices to predict interactions between transcription factors (TFs) and target genes.

Running Method

SDAS TF --input test.h5ad --output TF_result --label_key anno_cell2location --slice_key group --celltype_list celltype.txt --species human --n_cpus 24

Input Parameter Description

Parameter	Required	Default	Description
-i/--input	Yes		Input h5ad file (can be filtered)
-o/--output	Yes		Output folder, will be created automatically if not exists
--label_key	Yes		Specify the obs column name for cell type or grouping in h5ad.obs
--gene_symbol_key	No	real_gene_name	Specify the column name representing gene names (symbol) in h5ad
--slice_key	No		Column name for hierarchical grouping in h5ad.obs
--celltype_list	No		Path to cell type list file for analysis, cell types need >=2
--TF_list	No		Path to TF list file to focus on
--species	No	human	Species, human/mouse
--db_names	No		motif/regulatory database file path, e.g. hg38/10kbp*.feather
--motif	No		motif annotation file path, e.g. hg38/motifs-*.tbl
--n_cpus	No	24	Number of parallel threads
--method	No	grnboost2	GRN inference method, grnboost2/genie3

Output Results Display

Result File	Description
<input>_filtered.h5ad	(Intermediate file) h5ad file filtered using target celltype types
<input>.loom	(Intermediate file) Cell-gene expression matrix file built based on h5ad, pyscenic input file
adj.tsv	(Intermediate file) Gene regulatory network edge file built by pyscenic, used for pyscenic ctx to build TF-targets network
sce_regulon.gmt	(Intermediate file) TF-targets network built by pyscenic, used for pyscenic aucell to calculate Regulons (regulatory elements) activity
sce_regulon_AUC.loom	Regulon regulatory result file output by pyscenic, activity score for each cell, used for subsequent visualization
Regulon_Heatmap.png/pdf	Regulon activity heatmap, showing regulon activity in various cells/groups
Binary_Regulon_Heatmap.png/pdf	Binary regulon activity heatmap, convenient for cell subpopulation specificity analysis
RSS.pdf/RSS_group*.png/pdf	Regulon specificity score RSS heatmap/group heatmap
Spatial_Activity_Maps.png/pdf	Regulon activity heatmap in space, only drawn when --TF_list parameter is specified

• Regulon activity heatmap: Regulon_Heatmap.png/pdf Each row represents a regulon, each column represents a cell/group, color indicates AUC activity score. Used to compare the activity of the same Regulons in different cells, find cell subpopulations with specific Regulon activation, etc.

• Binary regulon activity heatmap: Binary_Regulon_Heatmap.png/pdf Binary regulon activity heatmap, black indicates that the cell opens the Regulons, convenient for cell subpopulation specificity analysis.

• Regulon specificity score RSS heatmap/group heatmap: RSS.png/pdf RSS_group*.png/pdf Regulon specificity score RSS heatmap in different groups/cell types. Circle size indicates RSS level, color gradient indicates standardized Z-value size; each row corresponds to a regulatory element, each column corresponds to a cell type. Within the same cell type, the specificity RSS of regulatory elements can be directly compared, and Z-values can be compared between different cell types.

• Regulon spatial activity heatmap: Spatial_Activity_Maps.png/pdf Regulon activity distribution in space, only output when spatial transcriptome data and --TF_list parameter are input.