PCA Density Filter

PCA Density Filter#

Filters cells based on their density in PCA space. Can be useful to remove outliers, missannotated cells, or to get a more homogenous population.

Filter cells based on density in PCA space#

pca_density_filter_adata(adata[, use_layer, ...])

Filters pca_density_filter() that accepts AnnData as input.

pca_density_filter_main(data[, ...])

Calculate density contours for PCA-reduced data, return the density of all input data, and identify the indices of the variables that were included in the PCA.