msmu.pl.plot_missingness

Plot the cumulative distribution of feature completeness.

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".	required
layer	str | None	Quantification layer; None reads .X.	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

The x-axis is the percentage of samples with an observed value; the y-axis is the cumulative percentage of features at or below that completeness. 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_missingness(mdata, modality="protein")
fig.show()