msmu.pl.plot_upset

Show feature intersections across observation groups.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData containing the selected modality and observation metadata.	required
modality	str	Name of the modality to plot, such as "protein" or "psm".	'protein'
layer	str | None	Quantification layer; None reads .X.	None
subset	str | None	Optional value to select in subset_column before plotting.	None
subset_column	str | None	Observation column used for subset; omitted values use the same sample-identifier resolution as obs_column.	None
groupby	str | None	Grouping column in observation metadata (or feature metadata where supported). None uses the resolved obs_column.	None
obs_column	str | None	Sample identifier in mdata.obs. If omitted, uses .uns["plotting"]["default_obs_column"], then source name/source_name/sample/filename, then the observation index.	None
kwargs	str	Additional plotly layout options, for example width=800 or title_text="QC".	{}

Returns:

Type	Description
Figure	plotly Figure. Call .show() to display or .write_html("plot.html") to export.

Notes

Intersections are based on non-missing quantification. groupby must resolve to an observation grouping. Quantification and embeddings are unchanged. Resolving an existing sample-identifier column can convert that column in mdata.obs to categorical; pass a copy to preserve its dtype.

Examples:

import msmu as mm
fig = mm.pl.plot_upset(mdata, modality="protein")
fig.show()