Majority Voting

Majority voting

This module allows majority-voting per cell for multiple cell-assignments of labels. The main computation is the mode per cell across multiple columns in the AnnData object.

Environments

The following environments are needed for the different metrics. Depending on which metrics you want to run, you do not need to install all environments.

• scanpy

Configuration

DATASETS:
  test:
    input:
      majority_voting:
        file_1: test/input/pbmc68k.h5ad
        file_2: test/input/pbmc68k.h5ad
    majority_voting:
      columns:
        - bulk_labels
        - na_*
      threshold: 0.6

• columns: columns or patterns (parsable by re) of columns in .obs to consider for majority voting.

• threshold: threshold to determine whether a label has low consensus agreement. If the majority agreement (#major_label/#columns) is lower than threshold, it’s consider to have low consensus agreement.

Note: The main assumption of the columns is that the labels across columns are from the same (or mostly same) set of unique labels/

Output

Additionally to the predicted labels, the module evaluates how strongly cells agree on their consensus label, and produces summary files and plots describing agreement levels.

• <out_dir>/majority_voting/dataset~<datasets>/file_id~<file_id>.zarr: Updated AnnData object with consensus label (majority_consensus) based on the most common value across selected columns, alongside a measure of how many columns agree (majority_consensus_agreement), and a Boolean flag for low agreement (majority_consensus_low_agreement). This table is written to a TSV file named majority_consensus_agreement.tsv in the output plots folder.

• <image_dir>/majority_voting/dataset~<datasets>/file_id~<file_id>/majority_consensus_agreement.tsv: Summary statistic of majority voting containing fractions of cells for every consensus label and agreement level.

• <image_dir>/majority_voting/dataset~<datasets>/file_id~<file_id>/majority_consensus_frac.png: Agreement bar plot showing the fraction of cells that have low agreement for each consensus label.