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)
    p <- dimred_tsne(toy_data,
                     tax_level="phylum",
                     color="AGE",
                     shape="GROUP",
                     k="3D",
                     initial_dims=30,
                     perplexity=10,
                     datatype="logcpm")
    p

[Package animalcules version 1.0.6 Index]