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 intohtml_dir
. Ifport
is set, start an HTTP server in the background and servehtml_dir
onport
.By default, export all gene expression data from
adata.raw
, the annotationslouvain
,percent_mito
,n_genes
andn_counts
and the topnb_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 :
str
Path to directory for exported Cell Browser files. Usually these are the files
exprMatrix.tsv.gz
,meta.tsv
, coordinate files liketsne.coords.tsv
, and cluster marker gene lists likemarkers.tsv
. A filecellbrowser.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 :
list
ofstr
ordict
ofkey (str)
->`display label (str)` 2-D embeddings in
adata.obsm
to export. The prefix “X_
” or “X_draw_graph_
” is not necessary. Coordinates missing fromadata
are skipped. By default, these keys are tried: [“tsne”, “umap”, “pagaFa”, “pagaFr”, “pagaUmap”, “phate”, “fa”, “fr”, “kk”, “drl”, “rt”]. For these, default display labels are automatically used. For other values, you can specify a dictionary instead of a list, the values of the dictionary are then the display labels for the coordinates, e.g.{'tsne' : "t-SNE by Scanpy"}
- annot_keys :
list
ofstr
ordict
ofkey (str)
->`display label (str)` Annotations in
adata.obsm
to export. Can be a dictionary with key -> display label.- skip_matrix :
boolean
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 :
str
If this variable is set, the export will build html files from
data_dir
tohtml_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 directoryhtml_dir
/project_name
will be created and an index.html will be created underhtml_dir
for all subdirectories. Existing files will be overwritten. If do not to use html_dir, you can use the command line toolcbBuild
to build the html directory.- port :
int
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 underhtml_dir
. To kill the process, callcellbrowser.cellbrowser.stop()
.- do_debug :
boolean
Activate debugging output
Examples
See this tutorial.
- adata :