Actually, I'm realising the real problem here is that the boxplots are shifted to the right, which is why the third boxplot is outside of the dashed box... Any idea what might be causing that?

Awesome, thanks Florian. I will test it as soon as I have a chance.

(I resorted to the histogram in the meantime.)

Is it possible to hide this dashed frame completely?

Thanks Florian - I'm working on a minimal reproducible example and will get back to you.

Here we go:

library(Gviz)

# generate random data
set.seed(16)
seqnames <- paste0(sample(1:22, 100, replace=TRUE))
start <- sample(1000:10000, 100)
end <- start + sample(100:1000, 100)
values <- matrix(rexp(1700), 100)
colnames(values) <- paste(sample(c("Low", "Medium", "High"), 17, replace=TRUE), 1:17, sep=".")

# create GRanges
dataset <- cbind.data.frame(seqnames, start, end, values)
dataset <- GRanges(dataset)

# define some variables for plotting
gen <- "hg38"
chr <- "16"
from <- 5000
to <- 10000
groups <- factor(sub("(Low|Medium|High)\\.[0-9]+", "\\1", names(mcols(dataset))), levels=c("Low", "Medium", "High"))

# create DataTrack
dataset <- dataset[seqnames(dataset)==chr & start(dataset) >= from & end(dataset) <= to]
datatrack <- DataTrack(dataset, name="dataset", genome=gen, chromosome=chr, start=from, end=to, groups=groups, type="boxplot", legend=TRUE)

png("mwe.png", res=150, width=10*150, height=12*150)
plotTracks(datatrack, chromosome=chr, from=from, to=to, background.title="grey70")
dev.off()

You can see that in all cases the boxplots appear shifted to the right with some blank space on the left and the rightmost boxplot on the dashed boundary or beyond.

How can I fix this? I'm guessing this is due to how my GRanges object is built and/or the way groups in my DataTrack are defined?

Thank you.

OK, I've got a better, real-world example:

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(Gviz)
set.seed(16)

# create GRanges with one range corresponding to a gene
gen <- "hg38"
chr <- "chr12"
start <- 121429097
end <- 121581015
values <- matrix(rexp(17), 1)
colnames(values) <- paste(sample(c("Low", "Medium", "High"), 17, replace=TRUE), 1:17, sep=".")
dataset <- cbind.data.frame(chr, start, end, values)
dataset <- GRanges(dataset)

# define groups
groups <- factor(sub("(Low|Medium|High)\\.[0-9]+", "\\1", names(mcols(dataset))), levels=c("Low", "Medium", "High"))

# create tracks
grtrack <- GeneRegionTrack(TxDb.Hsapiens.UCSC.hg38.knownGene, genome=gen, chromosome=chr, start=start, end=end, collapseTranscripts="meta")
dtrack <- DataTrack(dataset, name="dataset", genome=gen, chromosome=chr, start=start, end=end, groups=groups, type="boxplot", legend=TRUE)

# plot
png("mwe.png", res=150, width=10*150, height=12*150)
plotTracks(list(grtrack, dtrack), chromosome=chr, from=start-25000, to=end+25000)
dev.off()

From what I can see, the dashed frame is correctly aligned to the gene, but the boxplots are clearly shifted to the right for some reason.

Interestingly, I also get this warning message when calling plotTracks():

Warning message:
In min(diff(unique(sort(x)))) :
  no non-missing arguments to min; returning Inf

Any idea on how to fix this?

Thanks!

Hi Florian,

Did you have a chance to look at this?

Thank you,

Enrico