.intensity_box_per_sample

proteopy.pl.intensity_box_per_sample(adata, layer=None, order_by=None, order=None, group_by=None, zero_to_na=False, fill_na=None, log_transform=None, z_transform=False, ylabel='Intensity', xlabel_rotation=90, order_by_label_rotation=0, show=True, ax=None, save=None, figsize=(8, 5), color_scheme=None)[source]

Plot intensity distributions as boxplots, either per observation or pooled by a categorical grouping.

Parameters:

  • adata (AnnData) – Proteomics AnnData.

  • layer (str, optional) – Key in adata.layers providing the matrix to plot. When None, use adata.X.

  • order_by (str, optional) – Column in adata.obs whose categories annotate observation groups in per-observation mode. Mutually exclusive with group_by.

  • order (Sequence[str], optional) – Explicit order of order_by categories. When group_by is provided, these values order the grouped categories on the x-axis.

  • group_by (str, optional) – Column in adata.obs used to pool observations into a single box per category. When None, each observation is shown individually.

  • zero_to_na (bool, optional) – Convert zero intensities to NaN before other transforms.

  • fill_na (float, optional) – Replace missing intensities with this value before transformations.

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

  • z_transform (bool, optional) – Standardize intensities per observation after the log transform.

  • ylabel (str, optional) – Label for the y-axis.

  • xlabel_rotation (float, optional) – Rotation angle for observation tick labels.

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

  • show (bool, optional) – Display the figure when True and a new axis is created.

  • ax (Axes, optional) – Axis to draw on. When None, a new figure and axis are created.

  • save (str | os.PathLike, optional) – Path to save the figure. None skips saving.

  • figsize (tuple of float, optional) – Figure size used when creating a new axis.

  • color_scheme (Any, optional) – Palette forwarded to proteopy.utils.matplotlib._resolve_color_scheme() for either grouped categories (group_by) or observation-level annotations (order_by).

Returns:

Axis containing the rendered boxplot.

Return type:

Axes