ggsave throws error in example code

[bkille]

> library(gggenomes)

# to inspect the example data shipped with gggenomes
> data(package="gggenomes")

> gggenomes(
  genes = emale_genes, seqs = emale_seqs, links = emale_ava,
  feats = list(emale_tirs, ngaros=emale_ngaros, gc=emale_gc)) |> 
  add_sublinks(emale_prot_ava) |>
  sync() + # synchronize genome directions based on links
  geom_feat(position="identity", size=6) +
  geom_seq() +
  geom_link(data=links(2)) +
  geom_bin_label() +
  geom_gene(aes(fill=name)) +
  geom_gene_tag(aes(label=name), nudge_y=0.1, check_overlap = TRUE) +
  geom_feat(data=feats(ngaros), alpha=.3, size=10, position="identity") +
  geom_feat_note(aes(label="Ngaro-transposon"), data=feats(ngaros),
      nudge_y=.1, vjust=0) +
  geom_wiggle(aes(z=score, linetype="GC-content"), feats(gc),
      fill="lavenderblush4", position=position_nudge(y=-.2), height = .2) +
  scale_fill_brewer("Genes", palette="Dark2", na.value="cornsilk3")

runs just fine, but the final command throws an error

> ggsave("emales.png", width=8, height=4)
Error in guides$setup(scales, aesthetics, default = params$guide_default %||%  : 
  attempt to apply non-function

I've ran into this on both Ubuntu 22 and MacOS, both with R 4.3.2. Should I be using an earlier version of R? Thank you!

[buiguesj]

I'm getting the same error using my data, any solution??

[thackl]

Hi, thanks for reporting this. What ggplot version are you using?

[buiguesj]

I'm using ggplot2 3.5.0

[thackl]

OK, it cannot reproduce it in ggplot2 v3.4.4. Looking into v3.5.0 asap.

[Daniel-Ze]

For me running the example from the README.md file results in the same error as @bkille described however not after the ggsave command:

library(gggenomes)

# to inspect the example data shipped with gggenomes
data(package="gggenomes")

gggenomes(
  genes = emale_genes, seqs = emale_seqs, links = emale_ava,
  feats = list(emale_tirs, ngaros=emale_ngaros, gc=emale_gc)) |> 
  add_sublinks(emale_prot_ava) |>
  sync() + # synchronize genome directions based on links
  geom_feat(position="identity", size=6) +
  geom_seq() +
  geom_link(data=links(2)) +
  geom_bin_label() +
  geom_gene(aes(fill=name)) +
  geom_gene_tag(aes(label=name), nudge_y=0.1, check_overlap = TRUE) +
  geom_feat(data=feats(ngaros), alpha=.3, size=10, position="identity") +
  geom_feat_note(aes(label="Ngaro-transposon"), data=feats(ngaros),
                 nudge_y=.1, vjust=0) +
  geom_wiggle(aes(z=score, linetype="GC-content"), feats(gc),
              fill="lavenderblush4", position=position_nudge(y=-.2), height = .2) +
  scale_fill_brewer("Genes", palette="Dark2", na.value="cornsilk3")

ggsave("emales.png", width=8, height=4)

Output:

> data(package="gggenomes")
> gggenomes(
+   genes = emale_genes, seqs = emale_seqs, links = emale_ava,
+   feats = list(emale_tirs, ngaros=emale_ngaros, gc=emale_gc)) |> 
+   add_sublinks(emale_prot_ava) |>
+   sync() + # synchronize genome directions based on links
+   geom_feat(position="identity", size=6) +
+   geom_seq() +
+   geom_link(data=links(2)) +
+   geom_bin_label() +
+   geom_gene(aes(fill=name)) +
+   geom_gene_tag(aes(label=name), nudge_y=0.1, check_overlap = TRUE) +
+   geom_feat(data=feats(ngaros), alpha=.3, size=10, position="identity") +
+   geom_feat_note(aes(label="Ngaro-transposon"), data=feats(ngaros),
+                  nudge_y=.1, vjust=0) +
+   geom_wiggle(aes(z=score, linetype="GC-content"), feats(gc),
+               fill="lavenderblush4", position=position_nudge(y=-.2), height = .2) +
+   scale_fill_brewer("Genes", palette="Dark2", na.value="cornsilk3")
Transforming sublinks with "aa2nuc". Disable with `.transform = "none"`
Flipping: Cflag_017B,BVI_069,BVI_008A
wiggle bounds
• mid:  0.38
• low:  0.2
• high: 0.76
Error in guides$setup(scales, aesthetics, default = params$guide_default %||%  : 
  attempt to apply non-function
>

MacOS 13.6 Rstudio: Version 2023.12.1+402 (2023.12.1+402) R: 4.3.2 ggplot2: 3.5.0

[EpfeiferNutri]

I am getting the same error using ggplot2 v3.5.0 and v3.4.4. (both in R: 4.3.2, RStudio Server 2023.03.1)

Hoping for a fast and easy solution... thanks in advance (like this tool a lot!)!! :)

[thackl]

Should be fixed now by #178.

ggplot 3.5.0 introduced additional ggprotos for guides and layout, which gggenomes now also creates.

[EpfeiferNutri]

Thanks a lot! It is working now!