scirpy.tl.alpha_diversity#
- scirpy.tl.alpha_diversity(adata, groupby, *, target_col='clone_id', metric='normalized_shannon_entropy', inplace=True, key_added=None, airr_mod='airr', **kwargs)#
Computes the alpha diversity of clonotypes within a group.
Use a metric out of
normalized_shannon_entropy
,D50
,DXX
, and scikit-bio’s alpha diversity metrics. Alternatively, provide a custom function to calculate the diversity based on count vectors as explained here http://scikit-bio.org/docs/latest/diversity.html- Normalized shannon entropy:
Uses the Shannon Entropy as diversity measure. The Entrotpy gets normalized to group size.
- D50:
D50 is a measure of the minimum number of distinct clonotypes totalling greater than 50% of total clonotype counts in a given group, as a percentage out of the total number of clonotypes. Adapted from https://patents.google.com/patent/WO2012097374A1/en.
- DXX:
Similar to D50 where XX indicates the percentage of total clonotype counts threshold. Requires to pass the
percentage
keyword argument which can be within 0 and 100.
Ignores NaN values.
- Parameters:
adata (
Union
[AnnData
,MuData
,DataHandler
]) – AnnData or MuData object that contains AIRR information.groupby (
str
) – Column ofobs
by which the grouping will be performed.target_col (
str
(default:'clone_id'
)) – Column on which to compute the alpha diversitymetric (
str
|Callable
[[ndarray
],int
|float
] (default:'normalized_shannon_entropy'
)) – A metric used for diversity estimation out ofnormalized_shannon_entropy
,D50
,DXX
, any of scikit-bio’s alpha diversity metrics, or a custom function.inplace (
bool
(default:True
)) – IfTrue
, a column with the result will be stored inobs
. Otherwise the result will be returned.key_added (
Optional
[str
] (default:None
)) –Key under which the result will be stored in
obs
, ifinplace
isTrue
. When the function is running onMuData
, the result will be written to bothmdata.obs["{airr_mod}:{key_added}"]
andmdata.mod[airr_mod].obs[key_added]
.Defaults to
alpha_diversity_{target_col}
.airr_mod (
str
(default:'airr'
)) – Name of the modality with AIRR information is stored in theMuData
object. if anAnnData
object is passed to the function, this parameter is ignored.**kwargs – Additional arguments passed to the metric function.
- Return type:
- Returns:
Depending on the value of inplace returns a DataFrame with the alpha diversity for each group or adds a column to
adata.obs
.