limma: plotExonJunc – R documentation

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plotExonJunc

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

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)

limma

Linear Models for Microarray Data

v3.46.0

GPL (>=2)

Authors

Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]

Initial release

2020-10-19