plotLatentTranscripts {ballgown} | R Documentation

## cluster assembled transcripts and plot the results

### Description

This is an experimental, first-pass function that clusters assembled transcripts based on their overlap percentage, then plots and colors the transcript clusters.

### Usage

    plotLatentTranscripts(gene, gown, method = c("hclust", "kmeans"), k = NULL,
      choosek = c("var90", "thumb"), returncluster = TRUE,
      labelTranscripts = TRUE, ...)

### Arguments

`gene` | string, name of gene whose transcripts should be clustered (e.g., "XLOC_000001")
`gown` | object of class `ballgown` being used for analysis
`method` | clustering method to use. Currently can choose from hierarchical clustering (`hclust`) or K-means (`kmeans`). More methods are in development.
`k` | number of transcripts clusters to use. By default, `k` is `NULL` and thus is chosen using a rule of thumb, but providing `k` overrides those rules of thumb.
`choosek` | if `k` is not provided, how should the number of clusters be chosen? Must be one of "var90" (choose a `k` that explains 90 percent of the observed variation) or "thumb" (`k` is set to be approximately `sqrt(n)`, where n is the total number of transcripts for `gene`)
`returncluster` | if TRUE (as it is by default), return the results of the call to `clusterTrancsripts` so the data is available for later use. Nothing is returned if FALSE.
`labelTranscripts` | if TRUE (as it is by default), print transcript IDs on the y-axis
`...` | other arguments to pass to plotTranscripts

### Value

if `returncluster` is TRUE, the transcript clusters are returned as described in `clusterTranscripts`. A plot of the transcript clusters is also produced, in the style of `plotTranscripts`.

### Author(s)

Alyssa Frazee

### See Also

`clusterTranscripts`, `plotTranscripts`

### Examples

    data(bg)
    plotLatentTranscripts('XLOC_000454', bg, method='kmeans', k=2)

[Package ballgown version 2.18.0 Index]