deviationsTsne {chromVAR} | R Documentation

## deviationsTsne

### 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

[Package chromVAR version 1.9.0 Index]