thackl
commented
4 months ago Dear Tania,
thanks for reaching out.
The problem with your first error (genes + seqs) is that gggenomes only reads one thing from the fasta file with the sequence: the length, in your case 13000bp. But the coordinates of you genes are then 6107000. So when gggenomes tries to plot that, it cannot find any genes that fit on a 13000bp contig. If you want to zoom in on parts of sequences, you either not provide the sequence at all and gggenomes will just zoom in on the range of genes you provide, or you can explicitly set the length together with start end end for the sequence (which I did in the example below)
In the second case, you are reading your TE gff as seq= (second argument of gggenomes). What should work is z <- gggenomes(gff, feats=repeat_edta) + ....
This works for me (for the parts of the gffs that you provided)
# explicitly specify range of chromosome to plot
s0 <- tibble(
seq_id = "JAEVHH010000002.1",
length = 6107000,
start = 6094000,
end = 6107000
)
# read genes
g0 <- read_feats("genes.gff")
# read TE
t0 <- read_feats("te.gff")
gggenomes(g0, s0, t0) +
geom_gene() +
geom_seq() +
geom_feat(aes(color=type), data=feats(genes)) +
geom_bin_label() +
geom_seq_label() +
geom_gene() +
geom_feat()Hope that helps!
tania-k
Hello gggenomes folks.
I am currently attempting to run your program on my dataset that are subsections of:
Looks like:
FASTA (head)
GFF3 (head)
TE GFF3 (head)
Called as:
When running:
I receive
It has all my sequences on separate lines, but adding in any of the other two features, seq or repeat_edta throws errors.
z <- gggenomes(genes=gff, seqs=seq) + geom_gene() + geom_seq() + geom_feat(aes(color=type), data=feats(genes)) + geom_bin_label() + geom_seq_label() zOnly sawtype=NAin genes and will treat everything astype="CDS".Error inrequire_vars(): ! Required column(s) missing: • length Runrlang::last_trace()to see where the error occurred.My first error adding all three files gives me: `> p <- gggenomes(seqs = seq, genes = gff, feats = repeat_edta) + geom_seq() +
I am unsure how to progress.
I am running gggenomes on RStudio run through Linux/HPCC. I've updated ggplots2 to 3.5.0 and other dependencies along with restarting my R session.
Thank you for your time.