grassp.pl.marker_profiles_split

marker_profiles_split(adata, marker_column, plot_nan=False, n_columns=3, xticklabels=False, ylabel='Abundance', replicate_column=None, plot_mean=True, show=True, save=None)

Plot sample/fraction profiles grouped by marker annotation.

Creates a grid of subplots where each subplot shows profiles for all samples/fractions assigned to a specific marker category. Each line represents one sample/fraction’s profile across all proteins.

This function assumes that adata.var is sorted by Replicate (if present) and Fraction/Pulldown, so that related measurements are adjacent on the x-axis.

Parameters:

adata AnnData

AnnData object with proteins in .var and samples/fractions in .obs.

marker_column str

Column name in adata.obs containing marker annotations.

plot_nan bool (default: False)

If True, NaN entries in the marker column get their own facet; otherwise they are skipped.

n_columns int (default: 3)

Number of columns in the plot grid.

xticklabels bool (default: False)

If True, label x-ticks with adata.var_names.

ylabel str (default: 'Abundance')

Label for the y-axis. Default is 'Abundance'.

replicate_column str | None (default: None)

Column name in adata.var indicating replicate groups. If provided, vertical dashed lines are drawn at replicate boundaries (after the last instance of each replicate).

plot_mean bool (default: True)

If True (default), plot the mean profile across all samples/fractions in each category as a black line. A legend is added to the last subplot.

show bool (default: True)

If True (default) the plot is shown and the function returns None.

save bool | str | None (default: None)

If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {'.pdf', '.png', '.svg'}.

Return type:

Axes | None

Returns:

Returns the array of Axes if show is False, otherwise None.

See also

marker_profiles

Plot mean profiles with error bands in a single plot.