Question: ggbio tracks issue
0
gravatar for longoka
2.7 years ago by
longoka0
longoka0 wrote:

I'm using ggbio to plot multiple tracks; the code (shown below) worked fine two months ago, but now is throwing an error.

I've updated the ggbio package and looked for any hint of a change in the 'tracks' function that might explain the problem, to no avail. The individual plots (made using autoplot) display fine. A warning is thrown that implicit list embedding of S4 objects is deprecated, but I'm unsure how to remedy this.

Any hints?


Code:

p1 <- autoplot(txdb, aes(color = strand), which = gr1, gap.geom = "chevron")
p.rspos <- autoplot(vr[ix_snpoi], which = gr1, geom = "rect", arrow = TRUE)
p.expansion <- autoplot(expansion, which = gr1, geom = "rect")
tks <- tracks(C9orf72 = p1,
              Expan = p.expansion,
              RSPOS = p.rspos,
              heights = c(1,.5,.5)) + xlim(gr1)

print(tks)

Execution:

> tks <- tracks(C9orf72 = p1,
+               Expan = p.expansion,
+               RSPOS = p.rspos,
+               heights = c(1,.5,.5)) + xlim(gr1)
rect geom is used
Warning messages:
1: In `[<-`(`*tmp*`, names(args), value = <S4 object of class "GRanges">) :
  implicit list embedding of S4 objects is deprecated
2: In `[<-`(`*tmp*`, names(args), value = <S4 object of class "GRanges">) :
  implicit list embedding of S4 objects is deprecated
3: In `[<-`(`*tmp*`, names(args), value = <S4 object of class "GRanges">) :
  implicit list embedding of S4 objects is deprecated
ggbio tracks • 551 views
ADD COMMENTlink written 2.7 years ago by longoka0

Please provide a fully reproducible example. The new warnings are due to an update to R, and ggbio will need to adjust.

ADD REPLYlink written 2.7 years ago by Michael Lawrence11k
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