spliceRPlot {spliceR} | R Documentation |
Plot venn diagrams of alternative splicing events vs. samples.
spliceRPlot(spliceRobject, evaluate="nr_transcript", asType="All",colors=NULL, alpha=NULL, reset=FALSE, filters=NULL, expressionCutoff=0)
spliceRobject |
A |
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 |
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 |
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 |
expressionCutoff |
Numeric, giving the expression threshold (often in FPTKM) used for the 'expressedGenes' and 'expressedIso' filter. Default value is 0. |
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
.
A SpliceRList
, contianing additional temporary data for fast subsequent re-plotting.
Kristoffer Vitting-Seerup, Johannes Waage
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.
#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")