Introduction
Determining syntenic relationships between genomes is a important
step in understanding genome evolution. To do this, researchers align
species genomes to one another to detect sequence markers and conserved
sequences to identify syntenic regions. There is a plethora of tools
which can be used to identify this synteny such as DESCHRAMBLER.
However, they often return tables showing the orientation and, start and
stop positions of the syntenic regions which can often be hard to
interpret at face value.
Here, we provide a tool which visualises this data, improving the
interpretation of the alignment data, particularly for the
identification, characterization, and visualization of chromosome
rearrangements. SyntenyPlotteR relies on the use of ggplot2 to create
the graphics, producing three potential visualizations: a linear
relationship between syntenic regions of the genome using
draw.linear(), an evolution highway style grid showing
synteny between single chromosomes aligned between a single reference
species and one or more target species using draw.eh(), and
an ideogram with painted chromosomes to show syntenic relationships
between two genomes using draw.ideogram(). There is also a
function which can reformat data structured in the
DESCHRAMBLER/inferCARs format to a structure suitable for the required
input to the aforementioned functions using
reformat.syntenyData().
SyntenyPlotteR is solely designed to plot synteny data already
gathered by the user. This tool does not generate syntenic relationships
or curate data. As such, the user is required to construct syntenic
blocks, therefore, allowing the user to choose the most appropriate tool
for their needs. SyntenyPlotteR is easily implemented by the user with
single line functions taking directly the tab delimited files containing
the alignment data and chromosome lengths, thus meaning even
inexperienced users find the process fast to learn and simple to
use.
This package has been developed by Sarah Quigley (slq4@kent.ac.uk), Joana
Damas (joanadamas@gmail.com), Denis Larkin (dlarkin@rvc.ac.uk) and
Marta Farré (m.farre-belmonte@kent.ac.uk)
Evolution Highway style
The function outputs an image file containing the evolution highway
style alignment. As default the function saves the file to a temporary
directory, this can be overridden using the directory
parameter i.e. directory = "path/to/directory".
Usage
library(syntenyPlotteR)
draw.eh("output", chrRange, "data_file", fileformat = "png", colour = "lightblue", inverted.colour = "lightpink", w = 5.5, h = 10, ps = 10)
- output - String assigned to name of output file name
- chrRange - The range of chromosomes of the reference species this is
entered as either a single number i.e. 1 or a range of numbers
i.e. 1:22. Note: if you are inputting sex chromosomes or chromosomes
with characters in the name input a concatenated string
i.e. c(1,2,3,“X”)
- data_file - File containing the syntenic blocks of alignments of one
or more target species aligned to a single reference
There are optional parameters for some customization of this
function:
- fileformat - format for saving the image i.e. png or pdf, parameter
use:
fileformat = "pdf" (the default value is “png”)
- colour - colour of the syntenic blocks (not inverted blocks),
parameter use:
colour = "red" (the default value is
“lightblue”, see Rcolour pallette for colour options)
- inverted.colour - colour of the inverted syntenic blocks, parameter
use:
inverted.colour = "blue" (the default value is
“lightpink”, see Rcolour pallette for colour options)
- w - The width of the image created can be changed by using:
w = 5.5 (default)
- h - The height of the image created can be changed by using:
h = 10 (default)
- ps - The point size of the image created can be changed by using:
ps = 10 (default)
- directory - directory where to save image file
i.e.
directory = "path/to/directory" (default is save to
temporary directory)
Example code using data files in inst/extdata/
draw.eh("outputName", c(17,"X"), "example_eh_alignments_2.txt", fileformat = "pdf")
Example output:
Figure 5 - Example alignment in Evolution
Highway style. This figure shows chromosome 17 from a single reference
species aligned to three target species - sps1, sps2, and sps3. Sps1 and
sps2 chromosome 17 shows synteny with the reference chromosome 17
whereas sps3 chromosome 16 is syntenic to the reference chromosome 17.
The plot represents co-linear synteny with the blue shading and inverted
synteny with the pink shading. White space represents alignment
gaps.
Chromosome painting style
The function outputs an image file containing the chromosome painting
style alignment. As default the function saves the file to a temporary
directory, this can be overridden using the directory
parameter i.e. directory = "path/to/directory".
Usage
library(syntenyPlotteR)
draw.ideogram("file_data", "sizefile", "output", fileformat = "png", colours = colours.default, w=8.5, h=10, ps=5)
- file_data - file containing the syntenic blocks
- sizefile - tab separated file of all chromosome, scaffold, or contig
lengths and the species identifier, in order from first target species
in the alignment files followed by the first reference species in the
alignment files – top of file – to the last target species and reference
species in the alignment files – end of file.
- output - string assigned to the output file name
There are optional parameters for some customization of this
function:
- fileformat - format for saving the image i.e. png or pdf, parameter
use:
fileformat = "pdf" (the default value is “png”)
- colours - colours to assign to the ideograms in a concatenated
string of chromosome IDs with assigned colour values which can be found
with R colour Pallette, paramter use:
colours = c("1" = "red", "2" = "blue", "3" = "green","4" = "orange", "5" = "purple","X" = "grey")
if no colours are assigned default values will be used but colours MUST
be assigned to all chromosomes
- w - The width of the image created can be changed by using:
w = 5.5 (default)
- h - The height of the image created can be changed by using:
h = 10 (default)
- ps - The point size of the image created can be changed by using:
ps = 10 (default)
- directory - directory where to save image file
i.e.
directory = "path/to/directory" (default is save to
temporary directory)
Target is the species which chromosomes will be painted. Reference
will be used for painting and diagonals. Chromosomes will be in the same
order as in the target sizes file.
Note: If you have any alignments with chromosomes not defined in
the length file the function will not run.
Example code using data files in inst/extdata/
draw.ideogram("example_alignment_1.txt", "example_lengths.txt", "example.ideogram")
Example output:
Figure 6 - Example ideogram showing a comparison
between sps1 and sps2. In this figure sps1 is the target genome used to
draw the chromosome ideograms, and sps2 is the reference genome. Where
there is shared synteny between sps1 and sps2 the colours assigned to
the sps2 chromosomes are used to colour the syntenic regions i.e. sps1
chromosome 1 is drawn using the black box and the green shading shows
synteny with sps2 chromosome 1. Each syntenic block is traversed by a
diagonal line, identification of multiple syntenic blocks is shown where
there is a vertical line representing the end of one block and a start
of another, with a diagonal line in each syntenic block, whereas
completely syntenic chromosomes are depicted with a single line drawn
from the bottom left to top right such as with chromosome 1. Inverted
syntenic blocks are represented with a diagonal drawn from the top left
to the bottom right as seen in the first syntenic block of chromosome 19
- sps1 chromosome 19 ideogram drawn and coloured showing synteny with
sps2 chromosome 18.
Linear style
The function outputs an image file containing the linear style
alignment. As default the function saves the file to a temporary
directory, this can be overridden using the directory
parameter i.e. directory = "path/to/directory".
Usage
library(syntenyPlotteR)
draw.linear(output, sizefile, ..., fileformat = "png", colours = colours.default, w=13, h=5, opacity = .5)
- output - string assigned to the output file name
- sizefile - tab separated file of all chromosome, scaffold, or contig
lengths and the species identifier, in order from first target species
in the alignment files followed by the first reference species in the
alignment files – top of file – to the last target species and reference
species in the alignment files – end of file.
- … - files containing the syntenic blocks (one file per alignment, in
order from first target/reference (most recent species pairwise
alignment in ancestral reconstruction data) alignment file to last
target/reference (ancestor pairwise alignment in ancestral
reconstruction data) alignment file)
Please ensure any species identifiers used between length and
alignment files are matching (same identifiers and letter case)
There are optional parameters for some customization of this
function:
- fileformat - format for saving the image i.e. png or pdf, parameter
use:
fileformat = "pdf" (the default value is “png”)
- colours - colours to assign to the bands between ideograms in a
concatenated string of chromosome IDs with assigned colour values which
can be found with R colour Pallette, paramter use:
colours = c("1" = "red", "2" = "blue", "3" = "green","4" = "orange", "5" = "purple","X" = "grey")
if no colours are assigned default values will be used but colours MUST
be assigned to all chromosomes
- w - The width of the image created can be changed by using:
w = 5.5 (default)
- h - The height of the image created can be changed by using:
h = 10 (default)
- opacity - the opacity of the ribbons can be changes using inputting:
opacity = .5 (default)
- directory - directory where to save image file
i.e.
directory = "path/to/directory" (default is save to
temporary directory)
Note: If you have any alignments with chromosomes not defined in
the length file the function will not run.
Example code using data files in inst/extdata/
draw.linear("example_linear", "example_lengths.txt", "example_alignment_1.txt", "example_alignment_2.txt", "example_alignment_3.txt")
Example output:
Figure 7 - Example linear alignment plot between
four species, from sps4 through to sps1. The grey boxes represent the
chromosomes in each species genome, with the chromosome number written
above the box. The coloured bands represent synteny between the genomes
directly above/below one another. The colours of the bands represent the
reference chromosome that shares synteny with the target chromosome
i.e. chromosome 3 was assigned the colour pink thus any synteny
originating from chromosome 3 in either sps2, sps3, or sps4 to the
genome below will be shown by a pink band.
