scanpy.external.exporting.cellbrowser

scanpy.external.exporting.cellbrowser(adata, data_dir, data_name, embedding_keys=None, annot_keys=('louvain', 'percent_mito', 'n_genes', 'n_counts'), cluster_field='louvain', nb_marker=50, skip_matrix=False, html_dir=None, port=None, do_debug=False)

Export adata to a UCSC Cell Browser project directory. If html_dir is set, subsequently build the html files from the project directory into html_dir. If port is set, start an HTTP server in the background and serve html_dir on port.

By default, export all gene expression data from adata.raw, the annotations louvain, percent_mito, n_genes and n_counts and the top nb_marker cluster markers. All existing files in data_dir are overwritten, except cellbrowser.conf.

See UCSC Cellbrowser for details.

Parameters:

adata : AnnData

Annotated data matrix

data_dir : Union[Path, str]

Path to directory for exported Cell Browser files. Usually these are the files exprMatrix.tsv.gz, meta.tsv, coordinate files like tsne.coords.tsv, and cluster marker gene lists like markers.tsv. A file cellbrowser.conf is also created with pointers to these files. As a result, each adata object should have its own project_dir.

data_name : str

Name of dataset in Cell Browser, a string without special characters. This is written to data_dir/cellbrowser.conf. Ideally this is a short unique name for the dataset, like "pbmc3k" or "tabulamuris".

embedding_keys : Union[Iterable[str], Mapping[str, str], str, None] (default: None)

2-D embeddings in adata.obsm to export. The prefix X_ or X_draw_graph_ is not necessary. Coordinates missing from adata are skipped. By default (or when specifying 'all' or None), these keys are tried: ["tsne", "umap", "pagaFa", "pagaFr", "pagaUmap", "phate", "fa", "fr", "kk", "drl", "rt", "trimap"]. For these, default display labels are automatically used. For other values, you can specify a mapping from coordinate name to display label, e.g. {"tsne": "t-SNE by Scanpy"}.

annot_keys : Union[Iterable[str], Mapping[str, str], None] (default: ('louvain', 'percent_mito', 'n_genes', 'n_counts'))

Annotations in adata.obsm to export. Can be a mapping from annotation column name to display label. Specify None for all available columns in .obs.

skip_matrix : bool (default: False)

Do not export the matrix. If you had previously exported this adata into the same data_dir, then there is no need to export the whole matrix again. This option will make the export a lot faster, e.g. when only coordinates or meta data were changed.

html_dir : Union[str, Path, None] (default: None)

If this variable is set, the export will build html files from data_dir to html_dir, creating html/js/json files. Usually there is one global html output directory for all datasets. Often, html_dir is located under a webserver’s (like Apache) htdocs directory or is copied to one. A directory html_dir/project_name will be created and an index.html will be created under html_dir for all subdirectories. Existing files will be overwritten. If do not to use html_dir, you can use the command line tool cbBuild to build the html directory.

port : Optional[int] (default: None)

If this variable and html_dir are set, Python’s built-in web server will be spawned as a daemon in the background and serve the files under html_dir. To kill the process, call cellbrowser.cellbrowser.stop().

do_debug : bool (default: False)

Activate debugging output

Examples

See this tutorial.