dimred_umap {animalcules} | R Documentation

## Dimensionality reduction through PCA

### Description

Dimensionality reduction through PCA

### Usage

    dimred_umap(
      MAE,
      tax_level,
      color,
      shape = NULL,
      cx = 1,
      cy = 2,
      cz = NULL,
      n_neighbors = 15,
      metric = c("euclidean", "manhattan"),
      n_epochs = 200,
      init = c("spectral", "random"),
      min_dist = 0.1,
      datatype = c("logcpm", "relabu", "counts")
    )

### 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"
`cx` | Component on the x-axis e.g. 1
`cy` | Component on the y-axis e.g. 2
`cz` | Component on the z-axis e.g. 3
`n_neighbors` | Number of nearest neighbors
`metric` | Distance function e.g. c("euclidean", "manhattan")
`n_epochs` | Number of iterations
`init` | Initial embedding using eigenvector e.g c("spectral", "random")
`min_dist` | Determines how close points appear in the final layout
`datatype` | Datatype to use e.g. c("logcpm", "relabu", "counts")

### Value

A list with a plotly object and summary table

### Examples

    data_dir = system.file("extdata/MAE.rds", package = "animalcules")
    toy_data <- readRDS(data_dir)
    result <- dimred_umap(toy_data,
                          tax_level="genus",
                          color="AGE",
                          shape="DISEASE",
                          cx=1,
                          cy=2,
                          datatype="logcpm")
    result$plot

[Package animalcules version 1.8.1 Index]