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geom_link() is not working properly #195
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Hi. It seems to me that the seq id (e.g. VCI28MH2-S_0078) in your alignment is in a different format from the seq id in your fasta file (e.g. VCI28MH2-S) and gff file (e.g. VCI28MH2-S). I guess the seq id needs to match in order to infer any links. |
Dear Colleagues,
Thanks for your response. I somehow managed to do it by sniffing the
easyfig/mauve (#82) tutorial.
gggenomes is an excellent and powerful tool for comparing genomes.
Unfortunately, I am naive in R and I would request and recommend enriching
the documentation and tutorials.
But I really appreciate your efforts in solving queries case by case from
naive people like me.
Thanks.
…On Wed, Jul 10, 2024 at 12:09 PM Rikkiff ***@***.***> wrote:
Hi. It seems to me that the seq id (e.g. VCI28MH2-S_0078) in your
alignment is in a different format from the seq id in your fasta file (e.g.
VCI28MH2-S) and gff file (e.g. VCI28MH2-S). I guess the seq id needs to
match in order to infer any links.
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|
Great that you made it work. But can you confirm whether or not the issue was the seq ids of your alignment? |
Yes, it was related to the seq_id issue (apologies for delayed response). |
Hi, I am trying to create synteny between phages.
###upload files
s0 <- read_seqs("combined_contigs.fasta")
g0 <- read_feats("combined.gff")
colnames(g0)[18] <- "func"
gggenomes(genes=g0, seqs=s0) +
geom_seq() + geom_gene() + geom_bin_label() +
geom_gene(aes(fill=func)) +
scale_fill_brewer("Function", palette="Set3")
I used all vs all nuct blast, and uploaded it in r
l0 <- read.csv("homologs.txt", sep="\t", col.names = def_names("blast"))
drawing links
gggenomes(seqs=s0,genes=g0,links=l0) +
geom_seq() + geom_gene() + geom_seq_label() +
geom_link()
Now receiving the following error
Error in
geom_link()
:! Problem while computing aesthetics.
ℹ Error occurred in the 5th layer.
Caused by error in
.data$x
:! Column
x
not found in.data
.Run
rlang::last_trace()
to see where the error occurred.Warning message:
In layout_links(x, seqs, ...) :
No links found between adjacent genomes in provided order of genomes, consider reordering genomes
also can't use add_links() or add_sublinks() and receive the folloing error:
Error in UseMethod("add_sublinks") :
no applicable method for 'add_sublinks' applied to an object of class "data.frame"
I have 10 other phages to compare the synteny, the solution will save my life (I mean it). Thanks
data.zip
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