Reading data¶
In addition to various functions for reading input data in scanpy, various methods in picturedrocks need cluster labels.
-
picturedrocks.read.
process_clusts
(adata, name='clust', copy=False)¶ Process cluster labels from an obs column
This copies adata.obs[name] into adata.obs[“clust”] and precomputes cluster indices, number of clusters, etc for use by various functions in PicturedRocks.
Parameters: - adata (anndata.AnnData) –
- copy (bool) – determines whether a copy of AnnData object is returned
Returns: object with annotation
Return type: Notes
The information computed here is lost when saving as a .loom file. If a .loom file has cluster information, you should run this function immediately after
sc.read_loom
.
-
picturedrocks.read.
read_clusts
(adata, filename, sep=', ', name='clust', header=True, copy=False)¶ Read cluster labels from a csv into an obs column
Parameters: - adata (anndata.AnnData) – the AnnData object to read labels into
- filename (str) – filename of the csv file with labels
- sep (str, optional) – csv delimiter
- name (str, optional) – destination for label is adata.obs[name]
- header (bool) – deterimes whether csv has a header line. If false, it is assumed that data begins at the first line of csv
- copy (bool) – determines whether a copy of AnnData object is returned
Returns: object with cluster labels
Return type: Notes
- Cluster ids will automatically be changed so they are 0-indexed
- csv can either be two columns (in which case the first column is treated
as observation label and merging handled by pandas) or one column (only
cluster labels, ordered as in
adata
)