Here, we provide basic examples scripts for generating ribbon plots and chromosome sequence painting plots to visualize synteny blocks computed by ntSynt. Each R script script can be seen as a starting point, and can be customized as needed.
The R package gggenomes (https://thackl.github.io/gggenomes/) is used to generate ribbon plots to visualize multi-genome synteny blocks.
- Format the ntSynt synteny blocks for the ribbon plots R script using the provided script. Before running
format_blocks_gggenomes.sh, add thevisualization_scriptsdirectory to your PATH.
Usage: format_blocks_gggenomes.sh <synteny blocks TSV> <prefix> <length threshold> <assembly to use for colour> <FAI> <FAI> [FAI..]
The order of assembly FAI files will dictate the order of the genomes in the ribbon plots.
This script will generate two TSV files: {prefix}.links.tsv {prefix}.sequence_lengths.tsv
- Run the R script
- Required R packages: argparse, gggenomes, gtools, scales
usage: plot_synteny_blocks_gggenomes.R [-h] -s SEQUENCES -l LINKS [--scale SCALE] [-p PREFIX]
Plot the ntSynt synteny blocks using gggenomes
optional arguments:
-h, --help show this help message and exit
-s SEQUENCES, --sequences SEQUENCES
Input sequence lengths TSV
-l LINKS, --links LINKS
Synteny block links
--scale SCALE Length of scale bar in bases (default 1 Gbp)
-p PREFIX, --prefix PREFIX
Output prefix for PNG image (default
synteny_gggenomes_plot)
Example:
- These plots are highly customizable, so edit/adapt the script as needed!
ggplot2 is used to generate chromosome painting plots to visualize the multi-genome synteny blocks. Here, the synteny blocks for the other species are compared to a selected 'target' species. The segments based on the coordinate system of the 'target' species are coloured based on the chromosome of the other species. In addition, the relative orientation between the 'target' species and the other species is indicated by nudging the boxes up (forward) or down (reverse).
- Format the ntSynt synteny blocks for the chromosome painting R script using the provided script.
usage: format_blocks_chromosome_painting.py [-h] [--convert CONVERT] --target TARGET synteny_tsv
Formatting synteny blocks for chromosome painting
positional arguments:
synteny_tsv ntSynt-formatted synteny blocks TSV
optional arguments:
-h, --help show this help message and exit
--convert CONVERT TSV file with desired conversions for assembly names (optional)
--target TARGET Target assembly name
This script will output the results in standard out - pipe the output to a file.
- Run the R script
- Required R packages: argparse, ggplot2, dplyr, tidyr, gtools, scales
usage: plot_synteny_blocks-chromosome-painting.R [-h] -b BLOCKS [-g GAPS] [-p PREFIX]
Generate chromosome painting plots to visualize ntSynt synteny
optional arguments:
-h, --help show this help message and exit
-b BLOCKS, --blocks BLOCKS
ntSynt-formatted synteny blocks
-g GAPS, --gaps GAPS TSV file with gap coordinates. Required headers:
chrom, chromStart, chromEnd (optional)
-p PREFIX, --prefix PREFIX
Output prefix for PNG image (optional, default
synteny_chromosome)
- These plots can also be customized as needed (plot size, scale, comparing additional tools, etc.)
Example:
