dim_reduction: Perform dimensionality reduction

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

Description

Perform dimensionality reduction

Usage

dim_reduction(
  df,
  yvar,
  Ncells = NULL,
  transformation = NULL,
  y_trans = identity_trans(),
  perplexity = 50,
  dims = 2,
  method = "tSNE",
  check_duplicates = FALSE
)

Arguments

df	a data.frame with only numeric variables.
yvar	names of df's variables used to perform dimensionality reduction
Ncells	Maximum number of cells without any NA values sampled from df. If NULL, all cells without any NA values are used
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.
perplexity	t-SNE perplexity parameter (passed to Rtsne:Rstne())
dims	Number of dimensions (passed to Rtsne:Rstne())
method	Name of the method used. Either "tSNE" or "umap"
check_duplicates	logical. Checks whether duplicates are present (passed to Rtsne:Rstne())

Value

a data.frame with additionnal columns : "tSNE1" and "tSNE2" for method 'tSNE', "UMAP1" and "UMAP2" for method 'umap'

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