deviationsTsne: deviationsTsne

In chromVAR: Chromatin Variation Across Regions

Description

Perform tsne using bias corrected deviations to visualize either cell/sample similarity or motif/kmer/annotation similarity

Usage

deviationsTsne(object, threshold = 1.5, perplexity = if (what == "samples")
  30 else 8, max_iter = 1000, theta = 0.5, what = c("samples",
  "annotations"), shiny = FALSE)

Arguments

object	deviations result
threshold	variability threshold – use only deviations with variability greater than threshold
perplexity	perplexity parameter for tsne
max_iter	max iterations parameter for tsne
theta	theta parameter for tsne
what	tsne for similarity of samples or annotations?
shiny	load a shiny widget that enable you to explore perplexity and variability threshold parameter?

Value

data.frame with two columns for the two dimensions of tSNE output

Author(s)

Alicia Schep

Examples

# Load very small example results from computeDeviations
data(mini_dev, package = "chromVAR")
                         
tsne_res <- deviationsTsne(mini_dev, threshold = 0.8, shiny = FALSE)
# setting very low variabilitiy threshold because this is mini data set
# threshold should generally be above 1
# Use plotVariability to get a sense of an appropriate threshold

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.