graphST Algorithm

Usage

SDAS spatialDomain graphst –i st.h5ad –o outdir  --n_clusters 10 --bin_size 100 \
--gpu_id 1 --n_hvg 3000

Input Parameter Description

Parameter	Required	Default	Description
-i / --input	Yes		Stereo-seq h5ad, must contain the raw expression matrix
-o / --output	Yes		Output folder
--n_clusters	Yes		Number of clusters
--bin_size	Yes		Bin size, controls the size of points in the graph, not used for calculation, e.g., 20, 50, 100, cellbin (equivalent to 20)
--tool	No	mclust	Clustering method used by GraphST, options: 'mclust', 'leiden', 'louvain'
--layer	No		Layer in Stereo-seq h5ad where raw counts are stored
--n_hvg	No	3000	Number of highly variable genes
--slice_key	No		Name of the column in h5ad.obs indicating slice number for multi-slice data; must be specified for multi-slice analysis*
--gpu_id	No	-1	GPU ID to use; if -1, use CPU
--seed	No	42	Random seed

*Multi-slice analysis is possible under the following conditions:

1. Adjacent slices: For vertical tissue sections, spatial domain analysis requires slice registration. Set the slice_key parameter to the key in h5ad.obs that records multiple slices.

2. For a single tissue section divided horizontally into several consecutive slices and sequenced separately, horizontal registration is required for multi-slice analysis.

For details, refer to:

1. https://deepst-tutorials.readthedocs.io/en/latest/Tutorial%204_Horizontal%20Integration.html (Adjacent)

2. https://deepst-tutorials.readthedocs.io/en/latest/Tutorial%205_Vertical%20Integration.html (Horizontal)

Output Results

Result File	Description
<input_name>_domain_graphst.h5ad	Input h5ad + spatial domain clustering results, stored in obs['domain_graphst']
<input_name>_domain_graphst.png/pdf	Distribution plot of spatial domain clusters on the tissue, outputs both png and pdf
<input_name>_domain_graphst_split.png/pdf	Plots showing each spatial domain cluster separately, outputs both png and pdf

• Distribution plot of spatial domain clusters on the tissue: <input_name>_domain_graphst.png/pdf the color represents the spatial domain type of each bin/cellbin

• Separated distribution plots of spatial domain clusters on the tissue: <input_name>_domain_graphst_split.png/pdf the color represents the spatial domain type of each bin/cellbin, and the title indicates the spatial domain type (number of cells).