plotExonJunc {limma} | R Documentation

## Differential splicing plot with junctions

### Description

Plot differential usage results by exons and junctions for the specified gene and highlight the significantly spliced exons and junctions.

### Usage

    plotExonJunc(fit, coef=ncol(fit), geneid, genecolname=NULL, FDR=0.05, annotation=NULL)

### Arguments

`fit` | `MArrayLM` fit object produced by `diffSplice`. Must have the Entrez gene ids for all the exons and junctions stored in `fit$genes$GeneID`, length information for all the exons and junctions stored in `fit$genes$Length` and the strand information stored in `fit$genes$Strand`. To distinguish between exons and junctions, `fit$genes$Length` has to be set to 1 for all the junctions.
`coef` | the coefficient (column) of fit for which differentially splicing is assessed.
`geneid` | character string, ID of the gene to plot.
`genecolname` | column name of `fit$genes` containing `geneid`.
`FDR` | numeric, highlight exons and junctions with false discovery rate less than this cutoff. Red indicates up-regulation whereas blue indicates down-regulation. The FDR of the individual exon/junction is calculated based on the exon-level t-statistics test for differences between each exon/junction and all other exons/junctions for the same gene.
`annotation` | data frame containing the full exon annotation of the corresponding species. Must have the Entrez gene ids for all the exons stored in the `GeneID` column, start and end positions for all the exons stored in the `Start` and `End` columns, respectively.

### Details

Plot differential usage results by exons and junctions for the specified gene. The significantly spliced individual exons are highlighted as red blocks if up-regulated and blue blocks if down-regulated. All other exons are displayed as black blocks. The significantly spliced individual junctions are highlighted as red lines if up-regulated and blue lines if down-regulated. All other junctions are displayed as black lines.

Since the `diffSplice` analysis is usually performed after filtering, the full annotation (e.g. the inbuilt annotation in `featureCounts`) is highly recommended for producing the plot. When `annotation` is provided, the filtered exons are displayed as grey blocks.

### Value

A plot is created on the current graphics device.

### Author(s)

Yunshun Chen and Gordon Smyth

### See Also

`diffSplice`, `topSplice`

### Examples

    ## Not run:
    # diffSplice analysis
    v <- voom(dge, design)
    fit <- lmFit(v, design)
    ex <- diffSplice(fit, geneid="GeneID")

    # Get full annotation from Rsubread
    library(Rsubread)
    annotation.full <- getInBuiltAnnotation("mm10")

    # Make a plot
    plotExonJunc(ex, geneid="Foxp1", genecolname="Symbol", annotation=annotation.full)

    ## End(Not run)

[Package limma version 3.44.3 Index]