[R] How to tweak genomic plot with genoPlotR?

[Luigi Marongiu]

Already did...

On Tue, Apr 2, 2024 at 10:45 AM Eric Berger <ericjberger using gmail.com> wrote:
>
> According to https://cran.r-project.org/web/packages/genoPlotR/index.html
> the maintainer of genoPlotR is
>
> Lionel Guy <lionel.guy at imbim.uu.se>
>
> Send your question also to him.
>
> On Tue, Apr 2, 2024 at 11:27 AM Luigi Marongiu <marongiu.luigi using gmail.com> wrote:
> >
> > I would like to use your genoPlotR package
> > (doi:10.1093/bioinformatics/btq413) to compare the genomes of two
> > isolates of E. coli K-12 that I have. One is a K-12 that was in my
> > lab's fridge; the other is a derivative of K-12 bought some time ago,
> > HB101.
> > I tried to use genoPlotR, but I could not understand some functions
> > from your vignette. I would like to ask you whether you could help me
> > with this.
> >
> > I aligned the genomes (reference K-12 plus my isolates) with
> > `progressiveMauve --weight=15 --output=./K12_Aln.fa K12_multi.fa`,
> > where K12_multi.fa contains the fasta sequences of the reference and
> > the consensuses I obtained from my isolates after Illumina NGS. I then
> > ran this script:
> >
> > ```
> > ## get data
> > bbone_file = "./K12_Aln.backbone"
> > bbone = read_mauve_backbone(bbone_file, ref=2)
> > names(bbone$dna_segs) = c("K-12 ref.", "K-12 Ho", "HB101 Ho")
> >
> > ## calculate lengths
> > for (i in 1:length(bbone$comparisons)) {
> >   cmp = bbone$comparisons[[i]]
> >   bbone$comparisons[[i]]$length = abs(cmp$end1 - cmp$end1) +
> >                                   abs(cmp$end2 - cmp$end2)
> > }
> >
> > ## plot
> > plot_gene_map(dna_segs = bbone$dna_segs,
> >               comparisons = bbone$comparisons,
> >               global_color_scheme = c("length", "increasing", "red_blue", 0.7),
> >               override_color_schemes = TRUE)
> > ```
> > I got the following plot: https://u.cubeupload.com/Gigiux/Rplot.png
> > My questions are:
> > - How can I load the annotations? I have the K-12 annotations in gff3
> > and genebank formats, but how do I load them in the system so that I
> > plot it here?
> > - Is it possible to zoom in?
> > - Is it possible to change the color scheme?
> > Thank you
> >
> >
> >
> >
> > --
> > Best regards,
> > Luigi
> >
> > ______________________________________________
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> > and provide commented, minimal, self-contained, reproducible code.



-- 
Best regards,
Luigi