plotTsne: generate and plot tSNE

In hiddengenome/altum: deepG

Description

generate and plot tSNE

Usage

plotTsne(
  states,
  perplexity = c(0.5, 1),
  pca = TRUE,
  max_iter = 1000,
  path.metadata = NULL,
  sample.name.column = 1,
  label.name.column = 2,
  color.column = 3,
  out.path = "tsne.pdf"
)

Arguments

states	states for tSNE (generated by (extractCellFromStates())
perplexity	perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation)
pca	whether an initial PCA step should be performed (default: TRUE)
max_iter	number of iterations (default: 1000)
path.metadata	file used for coloring
sample.name.column	column in metadata file that holds the sample name
label.name.column	column that holds the label name in path.metadata
color.column	column that holds the color information in path.metadata
out.path	path to output pdf

hiddengenome/altum documentation built on April 22, 2020, 9:33 p.m.