lazyslide.tl.RNALinker

class RNALinker(agg_features, others, gene_name=None)

Bases: object

Link the aggregated WSI features with other omics data.

Parameters:

agg_featuresAnnData

The aggregated WSI features

othersAnnData

Other omics data, like RNA-seq, must have the same number of observations as agg_features.

gene_namestr, default: None

The key to use for the name of the omics data.

associate(method='linear_reg', score_key=None, key_added='association_score')

Associate scores with other omics.

associated_genes(n_genes=5, gene_name=None)

Get the top and bottom associated genes.

plot_rank(n_genes=5, gene_name=None)

Plot the rank of the association score.

plot_score(ax=None)

Plot the score distribution for the score group and others.

score(groupby, score_group, scale=True, test_method='t-test', n_features=100, key_added=None)

Score a group of samples based on the aggregated features.

The score will be higher for the score group and lower for the rest.

Parameters:

groupbystr

The key in the obs of agg_features.

score_groupstr

The specific group in the column of groupby to score.

scalebool, default: True

Scale the features between -1 and 1.

test_methodstr, default: “t-test”

The method to use for ranking omics features like genes.

n_featuresint | str, default: 100

The number of features to use for scoring. If “all”, use all features.

key_addedstr | None, default: None

The key to store the scores in the obs of agg_features. If not specify, f”{score_group}_score” will be added to the obs of agg_features.