spliceR (version 1.14.0)

spliceRPlot: Plot venn diagrams of alternative splicing events

Description

Plot venn diagrams of alternative splicing events vs. samples.

Usage

spliceRPlot(spliceRobject, evaluate="nr_transcript", asType="All",colors=NULL, alpha=NULL, reset=FALSE, filters=NULL, expressionCutoff=0)

Arguments

spliceRobject

A SpliceRList object, processed and returned by spliceR.

evaluate

A character, giving the evaulation criteria (see details).

asType

The alternative splicing type to visualize, either 'ESI','MEE','MESI','ISI','A5', 'A3','ATSS','ATTS' or 'All'. See spliceR for a full description of alternative splicing types.

colors

Character, giving plot colors for each condition. Must be same length as number of conditions. If NULL, colors from the ColorBrewer "Dark2" pallette is used.

alpha

A numeric between 0 and 1, giving the transparency of the plot. If NULL, the alpha will be set optimally depending on number of samples.

reset

A boolean, indicating whether to reinitialize the SpliceRList object for faster replotting.

filters

vector, giving the filters that should be applied - any combinations of 'geneOK', 'expressedGenes', 'sigGenes', 'isoOK', 'expressedIso', 'isoClass' and/or 'sigIso'. Works only for data from cufflinks, as a manually generated SpliceRList does not include these metacolumns.

expressionCutoff

Numeric, giving the expression threshold (often in FPTKM) used for the 'expressedGenes' and 'expressedIso' filter. Default value is 0.

Value

A SpliceRList, contianing additional temporary data for fast subsequent re-plotting.

Details

Upon inital usage of spliceRPlot, the SpliceRList is initiated with internal data, allowing for faster replotting. If the SpliceRList changes because of filtering or other manipulation, rerun spliceRPlot with reset=T. For the evaulate parameter, the following are valid: 'nr_transcript','nr_genes', 'nr_transcript_pr_gene', 'nr_AS', 'mean_AS_gene', 'mean_AS_transcript', 'mean_transcript_exp', 'mean_gene_exp'. 'nr_transcript' outputs number of transcripts, 'nr_AS' outputs number of alternative splicing events, 'mean_as' outputs the average number of AS events per gene, 'mean_transcript_exp' outputs the mean transcript expression and 'mean_gene_exp' output the mean gene expression. For a detailed description of filters, see spliceR.

References

Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.

Examples

#Load cufflinks example data
cuffDB <- prepareCuffExample()

#Generate SpliceRList from cufflinks data
cuffDB_spliceR <- prepareCuff(cuffDB)

#Reduce dataset size for fast example runtime
cuffDB_spliceR[[1]] <- cuffDB_spliceR[[1]][1:500]

#Run spliceR
mySpliceRList <- spliceR(cuffDB_spliceR, compareTo='preTranscript', filters=c('expressedGenes','geneOK', 'isoOK', 'expressedIso', 'isoClass'))

#Plot number of exon skipping/inclusion events 
mySpliceRList <- spliceRPlot(mySpliceRList, evaluate="nr_AS", asType="ESI")