dimred_tsne {animalcules} | R Documentation

## 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

[Package animalcules version 1.8.1 Index]