atlas.pl.plot_trends

atlas.pl.plot_trends(mudata, ptf, gene, time_key='pseudotime', fate_probability_key='fate_probabilities', branches=None, sharex=False, n_splines=8, n_points=200, order=1, save=None)

Plot branch-specific dynamics of transcription factor expression and gene activity.

This function fits branch-specific Generalized Additive Models (GAMs) using pygam.pygam.LinearGAM and visualizes smooth trends along pseudotime for a transcription factor (TF) and a target gene. Each lineage (branch) is modeled independently using fate probabilities as weights.

For each branch, the function displays the fitted GAM curve together with its confidence interval.

Parameters:

• mudata (MuData) – MuData object containing gene expression and gene activity modalities.

• ptf (str) – Name of the transcription factor in mudata["rna"].var_names.

• gene (str) – Name of the gene in mudata["activity"].var_names.

• time_key (str (default: 'pseudotime')) – Key in mudata.obs containing pseudotime values.

• fate_probability_key (str (default: 'fate_probabilities')) – Key in mudata.obsm containing fate probabilities for each branch.

• branches (list | str | None (default: None)) – Subset of branches to plot. If None, all available branches are shown.

• sharex (bool (default: False)) – Whether to share the x-axis (pseudotime) between the two subplots.

• n_splines (int (default: 8)) – Number of spline basis functions used in the GAM.

• n_points (int (default: 200)) – Number of points used to evaluate the fitted curves.

• order (int (default: 1)) – Currently unused parameter reserved for future extensions.

• save (str | None (default: None)) – If provided, saves the figure to figures/trends_<save>.png in the current working directory.

Return type:

None

Returns:

None The function generates a matplotlib figure and optionally saves it.