embed_cells: Embed Cells

In kgellatl/SignalCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This function will embed cells using sampleFactors() within reducedDim()

Usage

embed_cells(
  input,
  lem,
  embedding_key = NULL,
  method = "tSNE",
  comp_select = NULL,
  tSNE_perp = 30,
  iterations = 500,
  write_colData = T,
  colData_labs = NULL,
  seed = 100,
  print_progress = T
)

Arguments

input	the input sce
lem	a LEM within reducedDims() must be provided
embedding_key	The name of the embedding within metadata(reducedDim(input)) slot of SCE
method	the method for embedding. tSNE or OTHER?
comp_select	a vector of indices to use for embedding. NULL uses all, seq(1:10) would use first 10 sampleFactors withing the reducedDim(lem)
tSNE_perp	number of cells expressed above threshold for a given gene, 10-100 recommended.
iterations	The number of iterations for tSNE to perform.
write_colData	whether or not to write the embedding to colData
colData_labs	a vector of length 2 for the names of the X and Y colnames within colData()
seed	For tSNE, the seed. Can set to NULL if desired.
print_progress	will print progress if TRUE

kgellatl/SignalCell documentation built on Sept. 3, 2020, 8:45 a.m.