annotation_help.yaml Reference

This configuration file corresponds to --option=annotation_help and is used for marker statistics, spatial rendering, and pathway-enrichment support.

Parameter	Default	Description
option	advance_analysis	Stage identifier field stored in the file
results_folder	results	Root directory for analysis outputs
data_fold	data	Root directory for raw input data
sample_list	sample.txt	Path to the sample list file
run_type	visium	Platform type
channel	compare_analysis	Analysis channel
markers_algorithm	wilcoxon	Statistical method used for marker gene detection
shape_type	False	Keyword used to filter shape layer names
image_type	False	Keyword used to filter image layer names
species	human	Species background used for GO or KEGG enrichment
image_slice	False	Whether to crop the image
x1 / x2 / y1 / y2	0	Coordinates of the cropping window

Tuning suggestions

1. First confirm the appropriate markers_algorithm and species background species.

2. Enable image_slice and define coordinates only when reviewing a local tissue region.

3. For cross-sample comparisons, keep image_type and shape_type as consistent as possible.