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

Description Usage Arguments

View source: R/run_excyte.R

Description

Master function to run preprocessing,phenograph clustering and umap computation

Usage

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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


maximemeylan/Excyte documentation built on Nov. 10, 2020, 9:06 p.m.