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Last data update: 2014.03.03

R: cluster assembled transcripts and plot the results

plotLatentTranscripts

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

Examples


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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ballgown)

Attaching package: 'ballgown'

The following object is masked from 'package:base':

    structure

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ballgown/plotLatentTranscripts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotLatentTranscripts
> ### Title: cluster assembled transcripts and plot the results
> ### Aliases: plotLatentTranscripts
> 
> ### ** Examples
> 
> ## No test: 
> data(bg)
> plotLatentTranscripts('XLOC_000454', bg, method='kmeans', k=2)
$clusters
  cluster t_id
1       1 1294
2       2 1297
3       1 1301

$pctvar
[1] 0.9117737

> ## End(No test)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>