msmu.pl.plot_intensity

Plot intensity distributions for a modality.

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
groupby	str | None	Grouping column in observation metadata (or feature metadata where supported). None uses the resolved obs_column.	None
colorby	str | None	Observation column used to assign sample colors when groupby resolves to obs_column; ignored for other groupings. None uses the template palette.	None
ptype	str	"hist"/"histogram", "box"/"boxplot"/"simple_box"/"simplebox", or "vln"/"violin".	'hist'
template	str	Registered plotly template name, normally "msmu".	DEFAULT_TEMPLATE
bins	int	Number of histogram bins; ignored by box and violin plots.	30
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

Axes assume log2 intensities. Apply log2_transform beforehand when appropriate; this function does not log-transform 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_intensity(mdata, modality="protein", ptype="box")
fig.show()