PermutationTestReport (gesso.PermutationTestReport)

PermutationTestReport is a class that encapsulates the results of GESSO’s permutation-based hypothesis test for identifying spots with significantly elevated gene set activity scores (GASs).

class gesso.PermutationTestReport(geneset: str, permutation_test_df: DataFrame)[source]

Report object for storing GESSO permutation test results.

gas_df() → DataFrame[source]

Returns the geneset activity scores DataFrame.

Returns:

DataFrame containing the geneset activity scores.

Return type:

pd.DataFrame

htest_df() → DataFrame[source]

Returns the full permutation test DataFrame.

Returns:

DataFrame containing the full permutation test results. Contains four columns: ‘x’, ‘y’, ‘gas’, ‘p’.

Return type:

pd.DataFrame

locations_df() → DataFrame[source]

Returns the locations DataFrame.

Returns:

DataFrame containing the locations of the spots. Contains two columns: ‘x’ and ‘y’.

Return type:

pd.DataFrame

plot_gas_spatial_map(size: int = 20, cmap: Colormap | str = 'viridis', show_coords: bool = False, figsize: tuple[float, float] = (5.0, 5.0), ax: Axes | None = None) → Figure[source]

Plots the gene set activity scores of the permutation test across all locations.

Parameters:

  • size (int) – Default: 20. The size of the scatter points.

  • cmap (Colormap | None) – Default: “viridis”. The colormap to use for the scatter plot.

  • show_coords (bool) – Default: False. If True, shows the coordinates of the points.

  • figsize (tuple[float, float]) – Default: (5.0, 5.0). The size of the figure.

  • ax (plt.Axes | None) – Default: None. If None, creates a new figure.

plot_pval_spatial_map(size: int = 20, significance_threshold: float = 0.05, significant_color: str | Any = '#800080', not_significant_color: str | Any = '#D3D3D3', show_coords: bool = False, figsize: tuple[float, float] = (5.0, 5.0), ax: Axes | None = None) → Figure[source]

Plots the p-values of the permutation test across all locations.

Parameters:

  • size (int) – Default: 20. The size of the scatter points.

  • significance_threshold (float) – Default: 0.05. The threshold for significance.

  • significant_color (str) – Default: “#800080”. The color for significant points.

  • not_significant_color (str) – Default: “#D3D3D3”. The color for not significant points.

  • show_coords (bool) – Default: False. If True, shows the coordinates of the points.

  • figsize (tuple[float, float]) – Default: (5.0, 5.0). The size of the figure.

  • ax (plt.Axes | None) – Default: None. If None, creates a new figure.

pval_df() → DataFrame[source]

Returns the p-values DataFrame.

Returns:

DataFrame containing the p-values.

Return type:

pd.DataFrame