SubsampleAndTsne: Subsample data and run tSNE

In Sconify: A toolkit for performing KNN-based statistics for flow and mass cytometry data

Description

A wrapper for Rtsne that takes final SCONE output, and runs tSNE on it after subsampling. This is specifically for SCONE runs that contain large numbers of cells that tSNE would either be too time-consuming or messy for. Regarding the latter, tSNE typically appears less clean in the range of 10^5 cells

Usage

SubsampleAndTsne(dat, input, numcells)

Arguments

dat	tibble of original input data, and scone-based additions.
input	the markers used in the original knn computation, which are typically surface markers
numcells	the number of cells to be downsampled to

Value

a subsampled tibble that contains tSNE values

Examples

SubsampleAndTsne(wand.combined, input.markers, 500)

Sconify documentation built on Nov. 8, 2020, 6:45 p.m.