Tag: KaryoploteR

DOI: 10.18129/B9.bioc.karyoploteR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….

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Genome assembly and chromosome identification A Plantago ovata genome reference was generated by utilizing a total of 5.98 M (7 cells, 40.21 Gb, N50 = 10.45 Kb, 50 bp–121.17 Kb) PacBio long reads and 636.5 million (47.74 Gb) Hi-C short-reads. PacBio reads were used to assemble contigs, while Hi-C reads were used to achieve chromosome-level assembly. The final…

Hi all, I’d like to present karyoploteR, an R/Bioconductor package we have developed to plot any data on any genome in non-circular layouts. The goal of this project was to develop a tool as flexible as Circos, but easier to use and representing genomes as straight lines instead of circles,…

You can use the standard legend() command as outlined in this issue here: support.bioconductor.org/p/124328/ Minimal example based on bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfall.html : library(karyoploteR) somatic.mutations <- read.table(file=”ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Pancreas/Pancreas_raw_mutations_data.txt”, header=FALSE, sep=”t”, stringsAsFactors=FALSE) somatic.mutations <- setNames(somatic.mutations, c(“sample”, “mut.type”, “chr”, “start”, “end”, “ref”, “alt”, “origin”)) somatic.mutations <- split(somatic.mutations, somatic.mutations$sample) sm <- somatic.mutations[[“APGI_1992”]] sm.gr <- toGRanges(sm[,c(“chr”, “start”, “end”,…