pegasus.mark_doublets¶
- pegasus.mark_doublets(data, demux_attr='demux_type', dbl_clusts=None)[source]¶
Convert doublet prediction into doublet annotations that Pegasus can recognize. In addition, clusters in dbl_clusts will be marked as doublets.
Must run
infer_doublets
first.- Parameters
data (
pegasusio.MultimodalData
) – Annotated data matrix with rows for cells and columns for genes.demux_attr (
str
, optional, default:demux_type
) – Attribute indicating singlets/doublets that Pegasus can recognize. Currently this is ‘demux_type’, which is also used for hashing.dbl_clusts (
str
, optional, default: None) – Indicate which clusters should be marked as all doublets. It takes the format of ‘clust:value1,value2,…’, where ‘clust’ refers to the cluster attribute.
- Return type
None
- Returns
None
Update
data.obs
–data.obs[demux_attr]
: Singlet/doublet annotation.
Examples
>>> pg.mark_doublets(data, dbl_clusts='Annotation:B/T doublets')