deviationsTsne: deviationsTsne
In GreenleafLab/chromVAR: Chromatin Variation Across Regions

Description Usage Arguments Value Author(s) Examples

View source: R/dimensionality_reduction.R

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

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

`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?

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

Alicia Schep

# 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