karyoploteR

A tutorial and a set of examples on using the R/Bioconductor package karyoploteR to plot whole genomes with arbitrary data on them

karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.

 

karyoploteR is based on base R graphics and mimicks its interface. You first create a plot with a call to the plotKaryotype function and then sequentially call a number of plotting functions (kpLines, kpPoints, kpBars…) to add data to the genome plot.

karyoploteR is a plotting tool and only a plotting tool. That means that it is not able to download or retrieve any data. The downside of this is that the user is responsible of getting the data into R. The upside is that it is not tied to any data provider and thus can be used to plot genomic data coming from anywhere. The only exception to this are the ideograms cytobands, that by default are plotted using predownloaded data from UCSC.

karyoploteR is useful in any situation where a general genome-wide view of data is desirable. It can be used to plot somatic copy-number changes (SCNA) in cancer genomes obteined from exome, aCGH or SNP-array data; to plot the global BAM coverage from a WGS experiment; to create manhattan plots from GWAS studies; to create rainfall plots to detect kataegis. Since it is not tied to any data type or source, karyoploteR can be used to plot almost anything on a genome-wide scale.

Getting Started

karyoploteR is part of Bioconductor since version BioC 3.5. The package documentation, including the vignette and user manual is available at the karyoploteR’s Bioconductor landing page at http://bioconductor.org/packages/karyoploteR.

To install the package, start R and enter:

  source("https://bioconductor.org/biocLite.R")
  biocLite("karyoploteR")

Usign the development version

To use the development version of karyoploteR you should use the devel version of Bioconductor. The devel version of the package might work with release version of Bioconductor, althought that’s not expected to be always the case. You should be able to install the development version from the github repo using install_github() from the devtools package.

Citing karyoploteR

karyoploteR has been developed by Bernat Gel and Eduard Serra at IGTP Hereditary Cancer Group.

If you use karyoploteR in your research, please cite the Bioinformatics paper describing it:

Bernat Gel & Eduard Serra. (2017). karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics, 31–33. doi:10.1093/bioinformatics/btx346

Tutorial

The tutorial is a work in progress yet. Feel free to contact us to ask for any clarification or proposa a new section.

Ideograms and other non-data graphical elements

Low-level Plotting Functions

  • Overview of low-level plotting functions
  • Overview of the low-level plotting functions to plot basic graphical primitives (points, lines, arrows, poylgons...)

  • Points
  • Plot points to create scatter plots

  • Lines
  • Plot lines on the genome

  • Text
  • Add text labels on the data part of a karyoplot

  • Polygons
  • Add polygons to a karyoplot

  • Area
  • Plot a line and shade the area below

  • Segments
  • Plot segments on a karyoplot

  • Rectangles
  • Plot rectangles on a karyoplot

  • Arrows
  • Plot arrows on a karyoplot

  • Bars
  • Plot bars on a karyoplot

High-level Plotting Functions

Examples