get_cluster: Identify clusters

In VoisinneG/flowR: R-shiny interface for the analysis of flow cytometry data

Description

Identify clusters

Usage

get_cluster(
  df,
  yvar,
  transformation = NULL,
  y_trans = identity_trans(),
  dc = 3,
  alpha = 0.001,
  k = 100,
  k_meta = 8,
  scale = FALSE,
  method = "FlowSOM"
)

Arguments

df	a data.frame with only numeric variables.
yvar	names of df's variables used to find clusters
transformation	Named list of trans objects. List names should correspond to variable names.
y_trans	default trans object to be used if transformation is NULL.
dc	ClusterX dc parameter
alpha	ClusterX alpha parameter
k	integer; number of nearest neighbours (passed to Rphenograph())
k_meta	Maximum number of clusters to try out (passed to FlowSOM::MetaClustering())
scale	logical; Scale values before building SOM (for method 'FlowSOM' only)
method	Name of the method used. Either "FlowSOM", "ClusterX", "Rphenograph".

Value

a data.frame with the additionnal column "cluster"

VoisinneG/flowR documentation built on June 1, 2021, 6:42 p.m.