Input File Example

Expression Matrix File Format Description

• st.rds: Spatial transcriptomics expression matrix as a Seurat object, which must include the raw expression matrix, gene names, and other information. For details, please refer to SDAS input data format description. For multiple slices of spatial transcriptomics data, a custom slice_key can be provided (default is 'sampleID'), which is used for plotting (and for batch information in cell2location). If not provided, it is treated as a single slice.

• st.h5ad: Spatial transcriptomics expression matrix as an AnnData object, which must include spatial coordinates information, and the cell names (cell index) should be consistent with those in st.rds, used for spatial heatmap plotting. For details, please refer to SDAS input data format description.

Gene Chromosome Position File Format Description (Optional)

• --gene_order_file: User-defined gene chromosome position information file, which can be generated by gtf_to_position_file.py.

  • The --species parameter specifies the source of the gene_order_file for human/mouse, with row names as gene symbols:

    • human: GRCh38.p12- NCBI:GCA_000001405.27

    • mouse: GRCm38.p6-NCBI:GCA_000001635.8

Gene_symbol	chr	start	end
MIR1302-2HG	1	29554	31109
FAM138A	1	34554	36081
...	...	...	...