Perform t-SNE on a Specified Matrix and Store in Dimensionality Reduction Slot

Perform t-SNE on a Specified Matrix and Store in Dimensionality Reduction Slot

Usage

runTSNE(
  data,
  matrix_name = "Raw_Score",
  use_relevant = TRUE,
  n_pcs = 5,
  dims = 3,
  use_pcs = FALSE,
  seed = 42,
  ...
)

Arguments

data

An object of class CygnusObject containing an expression matrix.

matrix_name

Character string specifying the name of the matrix to use. Default is "Raw_Score".

use_relevant

Logical indicating whether to use only relevant markers. Default is TRUE.

n_pcs

Number of principal components. Used only when use_pcs = TRUE. Default is 5.

dims

Numeric value specifying the number of dimensions for t-SNE. Default is 2.

use_pcs

Logical indicating whether to use PCA results as input. Default is FALSE.

seed

Numeric value for setting a random seed. Default is 42.

...

Additional arguments to pass to the Rtsne function.

Value

The updated CygnusObject with t-SNE coordinates stored in the 'dim_red' slot.