compare_stage.yaml Reference

This configuration file corresponds to --option=compare_stage and is used for differential expression comparison and two-sample CellChat network comparison.

Parameter	Default	Description
option	compare_stage	Fixed stage identifier
results_folder / data_fold / sample_list	results / data / sample.txt	Output directory, data directory, and sample list
run_type / channel	visium / compare_analysis	Platform type and analysis channel
runpipe	compare_gene	Comparison branch, either compare_gene or cellchat
compare_algorithm	DEseq2	Differential expression algorithm
cell_focus	CAF	Cell type of interest
species	human	Species background used for enrichment
cellchat_compare_output_dir	results/compare_cellchat	Output directory for CellChat comparison results
cellchat_compare_sample_name1 / cellchat_compare_sample_name2	group_Non_Lesional / group_Lesional	Display names for the two groups
cellchat_compare_pathways	""	Specific pathways to compare
cellchat_compare_source_cells / cellchat_compare_target_cells	1,2,3 / 1,2,3	Sender and receiver cell selections
cellchat_compare_receiver_cells	1,2,3	Receiver-cell setting for aggregate plots
cellchat_compare_bubble_angle	45	Axis angle for bubble plots
cellchat_compare_bubble_remove_isolate	True	Whether to remove isolated nodes
cellchat_compare_do_ranknet / cellchat_compare_do_role_heatmap	True / False	Whether to output rankNet and role heatmap figures
cellchat_compare_do_pathway_plots / cellchat_compare_do_compare_overview	True / True	Whether to output pathway summary and overview comparison plots
cellchat_compare_do_compare_bubble / cellchat_compare_do_single_bubble	True / True	Whether to output paired-group and single-group bubble plots
cellchat_compare_do_gene_expression	False	Whether to output ligand-receptor expression plots
cellchat_compare_gene_colors	white,#FEC44F,#D95F0E	Color palette used for expression plots
cellchat_compare_gene_plot_type	dot	Expression plot type
cellchat_compare_save_merged	True	Whether to save the merged object

Tuning suggestions

1. When runpipe=compare_gene, focus first on compare_algorithm and cell_focus.

2. When runpipe=cellchat, first define the relevant source and target cell groups and the pathway set of interest.

3. If too many figures are being generated, temporarily disable selected cellchat_compare_do_* options for faster iteration.