popari.components.PopariDataset#
- class popari.components.PopariDataset(dataset, replicate_name, coordinates_key='spatial')[source]#
Wrapper around AnnData object. Allows for preprocessing of dataset for Popari.
- Parameters:
dataset (AnnData)
replicate_name (str)
coordinates_key (str)
- dataset#
AnnData dataset to convert into Popari-compatible object.
- replicate_name#
name of dataset
- coordinates_key#
location in
.obsmdataframe of 2D coordinates for datapoints.
Attributes
Methods
compute_spatial_neighbors([threshold])Compute neighbor graph based on spatial coordinates.
plot_metagene_embedding(metagene_index[, ...])Plot the embedding values for a embedding in-situ.
remove_connectivity_artifacts(...[, threshold])Remove artifacts in adjacency matrices produced by heuristic algorithms.