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ggsave throws error in example code #176
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I'm getting the same error using my data, any solution?? |
Hi, thanks for reporting this. What ggplot version are you using? |
I'm using ggplot2 3.5.0 |
OK, it cannot reproduce it in ggplot2 v3.4.4. Looking into v3.5.0 asap. |
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 |
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... |
Should be fixed now by #178. ggplot 3.5.0 introduced additional ggprotos for guides and layout, which gggenomes now also creates. |
Thanks a lot! It is working now! |
runs just fine, but the final command throws an error
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!
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