dimred_tsne: Dimensionality reduction through t-SNE

In compbiomed/animalcules: Interactive microbiome analysis toolkit

Dimensionality reduction through t-SNE

Description

Dimensionality reduction through t-SNE

Usage

dimred_tsne(
  MAE,
  tax_level,
  color,
  shape = NULL,
  k = c("2D", "3D"),
  initial_dims = 30,
  perplexity = 10,
  datatype = c("logcpm", "relabu", "counts"),
  tsne_cache = NULL
)

Arguments

MAE	A multi-assay experiment object
tax_level	The taxon level used for organisms
color	A condition to color data points by e.g. "AGE"
shape	A condition to shape data points by e.g. "SEX"
k	Plot dimensions e.g. c("2D","3D")
initial_dims	The number of dimensions to use in reduction method
perplexity	Optimal number of neighbors
datatype	Datatype to use e.g. c("logcpm", "relabu", "counts")
tsne_cache	Pass the cached data back into the function

Value

A list with a plotly object and cached data

Examples

data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
results <- dimred_tsne(toy_data,
  tax_level = "phylum",
  color = "AGE",
  shape = "GROUP",
  k = "3D",
  initial_dims = 30,
  perplexity = 10,
  datatype = "logcpm"
)
results$plot

compbiomed/animalcules documentation built on Feb. 7, 2024, 12:13 p.m.