Input File Example

h5ad Data Format Description

• st.h5ad: The AnnData object of the spatial transcriptomics expression matrix, which must contain raw expression matrix, spatial coordinates, and cell type annotation information. For details, please refer to SDAS Input Data Format Description.

cellchat Input File Description (Optional)

pathway.file Format Description:

• pathway.txt: Custom pathway file, no header, one pathway name per line.

COLLAGEN
FN1
LAMININ
JA

cellphonedb Input File Description (Optional)

microenvs_file_path Format Description:

• microenvs.txt: Custom microenvironment file, with header, two columns per line: cell type and spatial microenvironment, separated by tab.

cell_type	microenvironment
PV MMP11	Env1
PV MYH11	Env1
PV STEAP4	Env1

active_tfs_file_path Format Description:

• active_tfs.txt: Custom active transcription factor file, with header, two columns per line: cell type and TF, separated by tab.

cell_type	TF
EVT_1	ASCL2
EVT_1	ELK3
EVT_1	GATA3

degs_file_path Format Description:

• degs_file.txt: Custom differentially expressed gene file, with header, columns separated by tab. Only upregulated DEGs are provided, the first two columns must be cell type and gene, other columns are optional.

cell_type	gene	logFC	P.Value	adj.P.Val
GC	BGN	1.605019	3.950450e-131	4.844832e-127
GC	HLA-G	1.412923	5.616884e-254	6.888547e-250
GC	B2M	1.358709	0.000000e+00	0.000000e+00

cellphonedb_database Description

• SDAS built-in database source: https://github.com/ventolab/cellphonedb-data/tree/master, database version v5.0.0

• Custom database construction can refer to cellphonedb official tutorial: https://github.com/ventolab/CellphoneDB/blob/master/notebooks/T0_BuildDBfromFiles.ipynb