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lawremi
tracks(xlim) doesn't work with GRanges input
Hi,
derfinderPlot::plotCluster() is currently failing https://bioconductor.org/checkResults/release/bioc-LATEST/derfinderPlot/nebbiolo2-buildsrc.html and I traced it back to ggbio. Here's a small reproducible example that shows that tracks(xlim) fails if you pass it a GRanges object.
Best, Leo
library("ggbio")
data("hg19IdeogramCyto", package = "biovizBase", envir = environment())
p.ideogram <- plotIdeogram(hg19IdeogramCyto, "chr21")
p.ideogram
tracks(p.ideogram, xlim = GenomicRanges::GRanges("chr21:47409355-47409855"))
# Error in do.call(PlotList, PlotList) :
# 'what' must be a function or character string
traceback()
# 3: do.call(PlotList, PlotList)
# 2: do.call(PlotList, PlotList)
# 1: ggbio::tracks(p.ideogram, xlim = GenomicRanges::GRanges("chr21:47409355-47409855"))
options(width = 120)
sessioninfo::session_info()
# - Session info ------------------------------------------------------------------------------------------------------
# hash: flag: Zimbabwe, twelve o’clock, grinning face
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# setting value
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It seems it's failing against the GitHub Action might be related to some memory constraint not sure tho. To validate, I ran tests locally it was fine. So, Yes it should be fine to merge it.
Hi. It appears that this bug is still not fixed in version 1.42, when will you update the package with the correction?
