Subsampling base on geometric sketching — subsample

Subsamples the condor object to a predefined number of cells based on the geosketching algorithm (https://github.com/brianhie/geosketch). Using the PCA representation it subsamples your dataset by preserving the overall structure. Important, if you do not want to loose rare cell populations or do not want skew cell numbers. Requires the python package geosketch and reticulate.

Usage

subsample_geosketch(condor, pca_slot = "orig", n_sub = 0.5)

Arguments

condor: Flow cytometry dataset.
pca_slot: PCA slot to use for the sketching (e.g. "orig" or "norm").
n_sub: Number of cells to subset (default half of all cells).

Value

Returns a subsampled condor object