plotLatentTranscripts {ballgown} | R Documentation |
This is an experimental, first-pass function that clusters assembled transcripts based on their overlap percentage, then plots and colors the transcript clusters.
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 |
method |
clustering method to use. Currently can choose from
hierarchical clustering ( |
k |
number of transcripts clusters to use. By default, |
choosek |
if |
returncluster |
if TRUE (as it is by default), return the results of the
call to |
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
data(bg) plotLatentTranscripts('XLOC_000454', bg, method='kmeans', k=2)