API reference#

STDataset#

STDataset(count_df, coordinate_df[, ...])

STDataset: A meta class for discribing Spatial Transcriptomics data.

`load_10X`(read_path[, make_sparse])	Load 10X Genomics Space Ranger outputs and generate STDataset.
`load_anndata_h5`(read_path, **kwargs)	Load anndata saved h5ad file and generate STDataset.

run(dataset[, k, n_svgs, n_svg_clusters, cores])

Run all part of svgbit within one function.

`filters.low_variance_filter`(dataset[, var])	Filter genes with low variance.
`filters.high_expression_filter`(dataset[, ...])	Filter genes with high expression ratio.
`filters.quantile_filter`(dataset[, quantile])	Filter genes with quantile.

`normalizers.logcpm_normalizer`(dataset)	Perform logcpm on dataset.
`normalizers.cpm_normalizer`(dataset)	Perform CPM on dataset.

`plot.svg_heatmap`(dataset[, save_path, ...])	Draw SVG distribution heatmap.
`plot.spot_type_map`(dataset[, save_path, ...])	Draw SVG type map.
`plot.hotspot_distribution_map`(dataset, cluster)	Draw hotspot distribution map for one SVG cluster.
`plot.hotspot_expression`(dataset, gene[, ...])	Draw hotspot expression for one gene.
`plot.gene_expression`(dataset, gene[, ...])	Draw expression for one gene.
`plot.hotspot_colocalization_map`(dataset, genes)	Draw hotspot expression for multiple genes.

find_combinations(dataset, center_spots[, ...])

Find gene pairs in certain SVG cluster.

`STDataset.acquire_weight`([k])	Acquire weight for analysis.
`STDataset.acquire_hotspot`(**kwargs)	Acquire hotspot matrix.
`STDataset.acquire_density`([cores])	Acquire local Di and global AI value.
`STDataset.find_clusters`([n_svgs, ...])	Find SVG clusters.

`STDataset.AI`	A Series for AI value.
`STDataset.Di`	A DataFrame for local Di value.
`STDataset.coordinate_df`	Coordinate information.
`STDataset.count_df`	Expression matrix.
`STDataset.svg_cluster`	SVG cluster result.
`STDataset.spot_type`	A pd.DataFrame for spot type.
`STDataset.genes`	An Index for genes' names.
`STDataset.hotspot_df`	Hotspot matrix.
`STDataset.n_genes`	Number of total genes.
`STDataset.n_spots`	Number of total spots.
`STDataset.spots`	An Index for spots' names.
`STDataset.weight`	Weight used by svgbit.
`STDataset.weight_type`	What kind of weight is used.

`core.cluster.cluster`(hotspot_df, AI_series)	Cluster SVGs using hotspot matrix.
`core.density.hotspot_AI`(hotspot_df, ...[, cores])	Calculate Spatial Transcriptomics AI value for all genes.
`core.moran.local_moran`(gene_expression_df, ...)	Calculate local moran for hotspot identification.
`core.moran.global_moran`(gene_expression_df, ...)	Calculate global Moran's I value.