.peptide_intensities

proteopy.pl.peptide_intensities(adata, protein_ids=None, order_by=None, order=None, groups=None, facet_by=None, color=None, group_by=None, log_transform=None, fill_na=None, z_transform=False, show_zeros=True, xlab_rotation=0, order_by_label_rotation=0, figsize=(15, 6), show=True, save=None, ax=None, color_scheme=None)[source]

Plot peptide intensities across samples for the requested proteins.

Parameters:

  • adata (AnnData) – Proteomics AnnData.

  • protein_ids (str | Sequence[str]) – Show peptides mapping to this protein_id.

  • order_by (str, optional) – Column in adata.obs used to group and order observations on the x-axis. When None, observations follow adata.obs_names.

  • order (Sequence[str], optional) – Explicit order of groups (when order_by is set) or observations (when order_by is None).

  • groups (str | Sequence[str], optional) – Restrict order_by to selected categorical levels (requires order_by). The provided order determines the plotting order unless order is supplied.

  • facet_by (str | list[str | None], optional) – Columns in adata.obs used to split samples across a subplot grid. A string is coerced to [facet_by, None]. A list must contain exactly two elements: the row annotation followed by the column annotation. Either element may be None to collapse that grid axis. Within each facet, order_by groups and orders only the samples in that facet. Cannot be combined with ax.

  • color (str, optional) – adata.var column used for per-peptide coloring.

  • group_by (str, optional) – adata.var column whose categories are aggregated into a single line. Mutually exclusive with color; each group is colored via color_scheme.

  • log_transform (float, optional) – Logarithm base (>0 and !=1). Values are transformed as log(value + 1, base).

  • fill_na (float, optional) – Replace missing intensities before zero/log/z transformations when set.

  • z_transform (bool, optional) – Standardize each peptide across observations after optional log transform. Skips NA.

  • show_zeros (bool, optional) – Display zero intensities when True; otherwise zeros become NaN.

  • xlab_rotation (float, optional) – Rotation angle (degrees) applied to x-axis tick labels.

  • order_by_label_rotation (float, optional) – Rotation angle for the group labels drawn above grouped sections.

  • figsize (tuple[float, float], optional) – Size of each panel. Faceted figures scale this size by the number of subplot columns and rows.

  • color_scheme (Any, optional) – Palette specification forwarded to proteopy.utils.matplotlib._resolve_color_scheme() for either the per-peptide color or aggregated group_by categories.

  • show (bool, optional) – Display the generated figure(s) with matplotlib.pyplot.show().

  • save (str | os.PathLike, optional) – Path for saving the figure(s). Multi-protein selections are written to a PDF stack.

  • ax (matplotlib.axes.Axes, optional) – Axes object to plot onto. If None, create a new figure and axes. Cannot be combined with facet_by or multiple protein_ids.

Returns:

The Axes object used for one plot, or a list of Axes objects when multiple plots are created.

Return type:

Axes | list[Axes]