[R] How to tweak genomic plot with genoPlotR?

[Eric Berger]

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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