/syntenyPlotteR

R package to draw syntenic plots in 3 different styles

Primary LanguageR

syntenyPlotteR

R package to draw synteny plots in three different styles

This package has been developed by Joana Damas (joanadamas@gmail.com) and Marta Farré (m.farre-belmonte@kent.ac.uk)

To install:

devtools::install_github("marta-fb/syntenyPlotteR")

Input file

Please provide a file with the synteny blocks information, following this format, separated by tabs.

DO NOT include a header line

  • chr - chromosome of reference species -- it ONLY accepts numbers
  • start - start of block in reference species
  • end - end of block in reference species
  • tarChr - chromosome of target species
  • tarSt - start of block in target species
  • tarEnd - end of block in target species
  • orient - orientation of the block (1 or -1)
  • tarSpecies - name of the target species

Evolution Highway style

Usage

draw.eh("input file","output file name",chromosomeRange)

  • outputName - name of output file
  • chromosomeRange - range of chromosome numbers in reference species.

Example:

library(syntenyPlotteR)

draw.eh("syntenicBlocks_oneChromosome_severalSps.txt","testOut",1:1)

alt text

inferCARs style

Usage

library(syntenyPlotteR)
draw.ideogram("syntenicBlocks.txt", "reference_chr_size", "target_chr_size")

  • reference_chr_size Lenghts of reference chromosomes, scaffolds or contigs. Format: ID Length
  • target_chr_size Lenghts of target chromosomes, scaffolds or contigs. Format: ID Length

Example output:

alt text

Linear pairwise style

Usage

library(syntenyPlotteR)
draw.pairwise("syntenicBlocks.txt", "outputFileName", "reference_chr_size", "target_chr_size", "refName", "tarName")

  • outputFilename: Name of the output file
  • target_chr_size: Lenghts of target chromosomes, scaffolds or contigs. Format: ID Length
  • reference_chr_size: Lenghts of reference chromosomes, scaffolds or contigs. Format: ID Length
  • refName: name of the reference genome
  • tarName: name of the target genome

Example output:

alt text

To come soon:

  1. Update vignette
  2. Preprint in Biorxiv

Citation:

While we're preparing the publication, please cite:
Farré M, Kim J, et al. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Research 2019 Apr;29(4):576-589