DownsampleFCS: SPADE: density-dependent downsampling

In zunderlab/FLOWMAP: Graph-based visualizations of high-dimensional single-cell data across time

SPADE: density-dependent downsampling

Description

This code was adapted from the spade R package, available here: https://github.com/nolanlab/spade.

Usage

DownsampleFCS(fcs.file.names, clustering.var, channel.annotate,
  channel.remove, exclude.pctile = 0.01, target.pctile = 0.99,
  target.number = NULL, target.percent = 0.1, transform = TRUE)

Arguments

fcs.file.names	A vector of full file paths to the FCS files to be used
clustering.var	Vector naming channels to be used to calculate distances/differences between cells for clustering (if requested) and edge-drawing steps
channel.annotate	List mapping channel names to user-specified names to properly annotate all FCS file data
channel.remove	Vector naming channels to be removed from all loaded FCS data
exclude.pctile	Optional variable, numeric value for the downsampling_exclude_pctile variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
target.pctile	Optional variable, numeric value for the downsampling_target_pctile variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
target.number	Optional variable, numeric value for the downsampling_target_number variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
target.percent	Optional variable, numeric value for the downsampling_target_percent variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
transform	Logical specifying whether to transform the data using an Asinh transform typical of CyTOF/mass cytometry datasets, default is set to TRUE

Details

Specifically, the code in this file is adapted from downsample.R.

This code, authored by M. Linderman, P. Qiu, E. Simonds, Z. Bjornson, and maintained by Michael Linderman <[e-mail]>, was used under the GNU General Public License v. 2.0 (https://github.com/nolanlab/spade/blob/master/LICENSE) available here: https://opensource.org/licenses/GPL-2.0. In accordance with these license rules, our code is available under GPL-3.0.

UPDATE 12/17/19: Spade is no longer maintained We have included relevant function here to maintain functionality of FLOWMAP

zunderlab/FLOWMAP documentation built on Sept. 7, 2024, 6:31 p.m.