Hello, as per the title I'm struggling with generating a plot using plotExonJunc.

The error i'm getting is

Error in order(genes$Start, genes$End) : argument 1 is not a vector

I think the issue is with line 17 of the plotExonJunc function, it tries to order the genes by order(genes$Start, genes$End), however genes$Start/End do not exist, instead the columns are "ExonID" and "GeneID".

Here my code;

  library(limma)
  library(edgeR)

  # generate fake counts matrix
  set.seed(25)
  y <- matrix(rnbinom(4000,mu=5,size=2),ncol=4)
  dge <- DGEList(counts=y, group=rep(1:2,each=2))

  # list of Gene IDs
  GeneID <- c(rep(74355, 250), rep(18028, 250), rep(75605, 250), rep(75033, 250))

  # make fit using voom, voom 'design' defaults to unit vector
  v <- voom(dge)
  fit <- lmFit(v)

  # make diffSplice to plot
  ex <- diffSplice(fit, geneid = GeneID, verbose = FALSE)

  # plot diffSplice for gene 74355
  plotExonJunc(fit = ex, geneid = 74355)

Thanks for any help!

The plotExonJunc function requires the coordinates of the exons/junctions to produce the plot. In particular, it requires the start and end positions, as well as the length and strand information, of each feature to be stored in genes$Start, genes$End, genes$Length and genes$Strand of the fit object.

For example, the following code would produce an exon-junction plot as required:

library(limma)
library(edgeR)
# generate fake counts matrix
set.seed(25)
y <- matrix(rnbinom(200,mu=20,size=10),ncol=4)
dge <- DGEList(counts=y, group=rep(1:2,each=2))
dge$samples$lib.size <- rep(1e7,4)

# list of Gene IDs
GeneID <- c(rep(74355, 10), rep(18028, 10), rep(75605, 10), rep(75033, 10), rep(18029, 10))

# Generate start/end positions and calculate the length
Loci <- sort(sample(10000, 100))
Start <- Loci[2*(1:50)-1]
End <- Loci[2*(1:50)]
Length <- End - Start

# Make the second entry to be a junction (with a length of 1)
Start[2] <- End[1]
End[2] <- Start[3]
Length[2] <- 1

# Store information in the 'genes' component
genes <- data.frame(GeneID=GeneID, Start=Start, End=End, Length=Length, Strand="+")
dge$genes <- genes

# make fit using voom, voom 'design' defaults to unit vector
v <- voom(dge)
fit <- lmFit(v)

# make diffSplice to plot
ex <- diffSplice(fit, geneid = GeneID, verbose = FALSE)

# plot diffSplice for gene 74355
plotExonJunc(fit = ex, geneid = 74355)

We will revise the current documentation of the plotExonJunc function to give a better description of the usage.