compute_umap: Compute Umap coordinates for each event

In maximemeylan/Excyte: Exhaustive eXploration of CYTometry data

Description

Compute Umap coordinates for each event

Usage

compute_umap(
  processed_fcs_obj,
  channels = c("all", "with_desc")[1],
  k = 30,
  downsampling_umap = NULL,
  method = c("umap-learn", "naive")[1]
)

Arguments

processed_fcs_obj	list containing a datraframe of processed intensities for each event and informations of channel used
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.
k	numeric indicating the number of neighbor for phenograph and umap computation
downsampling_umap	numeric indicating the number of events to select to compute the umap
method	define if the umap should be computed with the python package (umap-learn) or with the naive R implementation

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