ovrlpy

Submodules

• ovrlpy.io

Attributes

SCALEBAR_PARAMS	Default scalebar parameters
UMAP_2D_PARAMS	Default 2D-UMAP parameters
UMAP_RGB_PARAMS	Default RGB-UMAP parameters

Classes

Ovrlp

Main analysis class for spatial overlap analysis.

Functions

plot_pseudocells(ovrlp, *[, umap_kwargs, ...])	Plots the UMAP and tissue side-to-side.
plot_region_of_interest(ovrlp, x, y, *[, window_size, ...])	Plot an overview of a zoomed-in region of interest.
plot_signal_integrity(ovrlp, *[, signal_threshold, ...])	Plots the determined signal integrity of the tissue sample in a signal integrity map.
plot_tissue(ovrlp, *[, scalebar, ax])	Plots the tissue colored by the UMAP embedding.
plot_umap(ovrlp, *[, annotate, ax])	Plots the UMAP embedding.
process_coordinates(coordinates, /[, gridsize, ...])	Runs the pre-processing routine of the coordinate dataframe.

Package Contents

ovrlpy.SCALEBAR_PARAMS: dict[str, Any]

Default scalebar parameters

ovrlpy.UMAP_2D_PARAMS: dict[str, Any]

Default 2D-UMAP parameters

ovrlpy.UMAP_RGB_PARAMS: dict[str, Any]

Default RGB-UMAP parameters