reduce_dim

reduce_dim

reduce_dim(x, method = "pca", dims = 2, ...)

# S3 method for SingleCellExperiment
reduce_dim(
  x,
  method = "pca",
  dims = 2,
  assay.name = "logcounts",
  coord.name = method,
  perplexity = NULL,
  initial_dims = 50,
  ...
)

# S3 method for matrix
reduce_dim(
  x,
  method = "pca",
  dims = 2,
  perplexity = 30,
  initial_dims = 50,
  ...
)

Arguments

x

matrix object.

method

tyoe of dimensionality reduction: pca, tsne, umap.

dims

number of dimensions to keep in final result.

...

arguments to be passed down to methods.

assay.name

name of assay slot.

coord.name

name of reducedDim slot.

perplexity

perplexity for tSNE.

initial_dims

initial PCA dimensions for tSNE.