Already did... On Tue, Apr 2, 2024 at 10:45 AM Eric Berger <ericjber...@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.lu...@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 > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code.
-- Best regards, Luigi ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
