msmu.pl.plot_var

Plot a feature annotation by group.

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".	'psm'
groupby	str | None	Grouping column in observation metadata (or feature metadata where supported). None uses the resolved obs_column.	None
var_column	str | None	Required column in the selected modality .var, such as "charge" or "purity".	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
ptype	str | None	"stack" (aliases "stackd", "stacked_bar"), "box", "simple_box"/"simplebox", "vln"/"violin", or "hist"/"histogram". None selects box for numeric columns with more than 20 distinct values, otherwise stacked bars.	None
bins	int	Histogram bin count; ignored for other plot types.	30
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 selected feature annotation must exist; numeric plot types require numeric values. 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_var(mdata, modality="psm", var_column="charge")
fig.show()