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_venn_plots

Venn and overlap-enrichment helpers from _plotting/_venn_plots.py.

Important package note: this module exists in _plotting/, but it is not currently re-exported by _plotting/__init__.py. Use a direct submodule import when needed.

from adata_science_tools._plotting._venn_plots import venn_plot_2list

Public functions

  • venn_plot_2list
  • venn_plot_3list
  • geneset_enrichment_venn
  • geneset_enrichemnt_ol_ven_M_n_N_x

venn_plot_2list

Creates a two-set Venn diagram and optionally returns a summary DataFrame.

Full signature

def venn_plot_2list(list1, list2,  set_label_list, plot_title,show_plot=True,return_df=True):
overlap_df = venn_plot_2list(
    list1=genes_a,
    list2=genes_b,
    set_label_list=["A", "B"],
    plot_title="Overlap of A and B",
    show_plot=True,
    return_df=True,
)

Important behavior:

  • Inputs are converted to Python sets before overlap calculation.
  • The returned DataFrame summarizes unique and shared members as stringified lists.
  • show_plot=False suppresses the Matplotlib rendering.

venn_plot_3list

Creates a three-set Venn diagram and optionally returns an overlap summary DataFrame.

Full signature

def venn_plot_3list(list1, list2, list3, set_label_list, plot_title,show_plot=False,return_df=False):

Important behavior:

  • Inputs are converted to sets.
  • The returned DataFrame keeps the Elements column as Python lists rather than strings.
  • The default arguments are show_plot=False and return_df=False.

geneset_enrichment_venn

Computes a hypergeometric enrichment p-value and displays a Venn diagram for:

Full signature

def geneset_enrichment_venn(universe, geneset, hits,
                            dataset_label="DEGs",
                            geneset_label="GeneSet",
                            plot_title="",
                            shift_overlap=True,
                            shift_overlap_labely=0.1):
  • universe
  • geneset
  • hits

The function returns a dict with:

  • M
  • n
  • N
  • x
  • p_enrichment
  • overlap

Important behavior:

  • All three inputs are intersected with the supplied universe.
  • The overlap label is rewritten to include the overlap count and enrichment p-value.
  • The function always shows the plot.

geneset_enrichemnt_ol_ven_M_n_N_x

This legacy helper also computes a hypergeometric enrichment display from three sets.

Full signature

def geneset_enrichemnt_ol_ven_M_n_N_x(
    M_set, n_set, N_set,
    dataset_label="dataset_label",
    geneset_label="geneset_label",
    plot_title="plot_title",
    shift_overlap=True,
    shift_overlap_labely=0.1
        ):

Important behavior:

  • The function name is misspelled in the source and docs to match the current API.
  • It prints the universe and overlap statistics.
  • It shows the plot.
  • The current implementation does not return a value.

Coverage note

This module is documented from source code rather than dedicated tests.