runtSNE — runtSNE • cyCONDOR

Calculate tSNE dimensionality reduction.

Usage

runtSNE(
  fcd,
  input_type,
  data_slot,
  perplexity = 30,
  seed = 91,
  prefix = NULL,
  nThreads = 1,
  nPC = ncol(fcd$pca[[data_slot]]),
  markers = colnames(fcd$expr[[data_slot]]),
  discard = FALSE
)

Arguments

fcd: flow cytometry dataset.
input_type: data to use for the calculation, e.g. "expr" or "pca" (suggested: "pca").
data_slot: data slot to use for the calculation, e.g. "orig" or "norm".
perplexity: Value that controls how many nearest neighbors are taken into account when constructing the embedding (see Rtsne documentation for details).
seed: A seed is set for reproducibility.
prefix: Optional prefix for the slot name of the output.
nThreads: Number of threads to be used in the tSNE calculation.
nPC: Number of principal components to use for the analysis.
markers: Vector of marker names to include or exclude from UMAP calculation according to the discard parameter. See functions used_markers and measured_markers for the extraction of markers directly from the condor object.
discard: Boolean to decide if the markers specified should be included, "F", or excluded, "T", from the UMAP calculation. Default = F.

Value

The function returns a fcd including a data frame with the tSNE coordinates saved in fcd$tSNE. The name of the output consists of the prefix (if given) and the data slot. If a nPC is given it will be added to the output name.

Details

runtSNE

See [Jesse H. Krijthe (2015). Rtsne: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation], (https://github.com/jkrijthe/Rtsne) for more details on the Rtsne method.