dimred_tsne: Dimensionality reduction through t-SNE

In animalcules: Interactive microbiome analysis toolkit

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

animalcules documentation built on Nov. 8, 2020, 6:47 p.m.