run_excyte: Master function to run preprocessing,phenograph clustering...

In maxmeyl/Excyte: Exhaustive eXploration of CYTometry data

Description

Master function to run preprocessing,phenograph clustering and umap computation

Usage

run_excyte(
  fcs_dir,
  downsampling = 3000,
  downsampling_umap = NULL,
  channels = "all",
  method = c("umap-learn", "naive")[1],
  k = 30
)

Arguments

fcs_dir	directory or vector containing fcs files to be used
downsampling	numeric indicating the number event to randomly select from each fcs, if the number of events request is bigger than the number of event in the fcs, all event are selected
downsampling_umap	numeric indicating the number of events to sample to compute the umap
channels	vector containing channels to select. Can be "all" to select all channels, "with_desc" to select channels with a marker description or a vector a channels.
method	define if the umap should be computed with the python package (umap-learn) or with the naive R implementation
k	numeric indicating the number of neighbor for phenograph and umap computation

maxmeyl/Excyte documentation built on Nov. 17, 2020, 8:09 a.m.