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Last data update: 2014.03.03

R: Plot venn diagrams of alternative splicing events

spliceRPlot

R Documentation

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.

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.

Value

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

Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(spliceR)
Loading required package: cummeRbund
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

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

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

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

    promoters

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

    promoters

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

    conditions

Loading required package: VennDiagram
Loading required package: futile.logger
Loading required package: RColorBrewer
Loading required package: plyr

Attaching package: 'plyr'

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

    count

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

    desc

The following object is masked from 'package:S4Vectors':

    rename


Attaching package: 'spliceR'

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

    conditions

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

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/spliceR/spliceRPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spliceRPlot
> ### Title: Plot venn diagrams of alternative splicing events
> ### Aliases: spliceRPlot
> 
> ### ** Examples
> 
> #Load cufflinks example data
> cuffDB <- prepareCuffExample()
Creating database /tmp/Rtmp5cgXNo/cuffData.db
Reading Run Info File /tmp/Rtmp5cgXNo/run.info
Writing runInfo Table
Reading Read Group Info  /tmp/Rtmp5cgXNo/read_groups.info
Writing replicates Table
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/Rtmp5cgXNo/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /tmp/Rtmp5cgXNo/gene_exp.diff
Writing geneExpDiffData table
Reading /tmp/Rtmp5cgXNo/promoters.diff
Writing promoterDiffData table
Reading /tmp/Rtmp5cgXNo/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in /tmp/Rtmp5cgXNo/genes.read_group_tracking
Writing geneReplicateData table
Reading /tmp/Rtmp5cgXNo/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /tmp/Rtmp5cgXNo/isoform_exp.diff
Writing isoformExpDiffData table
Reading /tmp/Rtmp5cgXNo/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in /tmp/Rtmp5cgXNo/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /tmp/Rtmp5cgXNo/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /tmp/Rtmp5cgXNo/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /tmp/Rtmp5cgXNo/splicing.diff
Writing splicingDiffData table
Reading /tmp/Rtmp5cgXNo/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in /tmp/Rtmp5cgXNo/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /tmp/Rtmp5cgXNo/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /tmp/Rtmp5cgXNo/cds_exp.diff
Writing CDSExpDiffData table
Reading /tmp/Rtmp5cgXNo/cds.diff
Writing CDSDiffData table
Reading /tmp/Rtmp5cgXNo/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in /tmp/Rtmp5cgXNo/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped 
2: attributes are not identical across measure variables; they will be dropped 
3: attributes are not identical across measure variables; they will be dropped 
4: attributes are not identical across measure variables; they will be dropped 
5: attributes are not identical across measure variables; they will be dropped 
6: attributes are not identical across measure variables; they will be dropped 
7: attributes are not identical across measure variables; they will be dropped 
8: attributes are not identical across measure variables; they will be dropped 
> 
> #Generate SpliceRList from cufflinks data
> cuffDB_spliceR <- prepareCuff(cuffDB)
Reading cuffDB, isoforms...
Reading cuffDB, exons...
Analyzing cufflinks annotation problem...
Fixing cufflinks annotation problem...
Cufflinks annotation problem was fixed for 65 Cuff_genes
Creating spliceRList...
> 
> #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'))
Preparing transcript data...
Converting to internal objects...
167 isoforms pre-filtering...
Filtering...
78 isoforms post-filtering...
Preparing exons...
Analyzing transcripts...
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Preparing output...
Done in 2.5 secs
> 
> #Plot number of exon skipping/inclusion events 
> mySpliceRList <- spliceRPlot(mySpliceRList, evaluate="nr_AS", asType="ESI")
Initializing (this will only happen once)...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>