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.