geom_link() is not working properly

[tahsinkhann]

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

[Rikkiff]

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.

[tahsinkhann]

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. — Reply to this email directly, view it on GitHub <#195 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKLILJKCOCJUINVFPFRSH33ZLUI53AVCNFSM6AAAAABKN432DCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRQGIZDQNBYHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Tahsin Khan *MPhil Student* University of Cambridge & Wellcome Sanger Institute Cambridge, United Kingdom Email: ***@***.***; ***@***.***

[Rikkiff]

Great that you made it work. But can you confirm whether or not the issue was the seq ids of your alignment?

[tahsinkhann]

Yes, it was related to the seq_id issue (apologies for delayed response).