dimred_tsne {animalcules} | R Documentation |
Dimensionality reduction through t-SNE
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 )
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 |
A list with a plotly object and cached data
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