plotLatentTranscripts: cluster assembled transcripts and plot the results
In ballgown: Flexible, isoform-level differential expression analysis

Description Usage Arguments Value Author(s) See Also Examples

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

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

`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

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.

Alyssa Frazee

clusterTranscripts, plotTranscripts