plotTsne: generate and plot tSNE

Description Usage Arguments

View source: R/tSNE.R

Description

generate and plot tSNE

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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/deepG documentation built on April 16, 2020, 1:38 a.m.