Comments (8)
Should be fixed now by #178.
ggplot 3.5.0 introduced additional ggprotos for guides and layout, which gggenomes now also creates.
from gggenomes.
OK, it cannot reproduce it in ggplot2 v3.4.4. Looking into v3.5.0 asap.
from gggenomes.
I'm getting the same error using my data, any solution??
from gggenomes.
Hi, thanks for reporting this. What ggplot version are you using?
from gggenomes.
I'm using ggplot2 3.5.0
from gggenomes.
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
from gggenomes.
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!)!! :)
from gggenomes.
Thanks a lot! It is working now!
from gggenomes.
Related Issues (20)
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- Error in eval(`_inherit`, env, NULL): object 'Guides' not found. HOT 1
- Error in guides$setup(scales, aesthetics, default = params$guide_default %||% : attempt to apply non-function HOT 1
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- Incorrect labels for scale with large sequences HOT 1
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- Multiple coverage tracks supported? HOT 4
- How can I change the distance (spacer) between different seqs? HOT 2
- Calculate coordinates from gff file with genes in different directions HOT 1
- Error when loading emales.fna with https://github.com/thackl/gggenomes/blob/HEAD/vignettes/emales.Rmd HOT 1
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