syntenyPlotteR (version 1.0.0)

draw.ideogram: Draw ideograms in chromosome painting style

Description

Draw synteny ideograms in Chromosome painting style

Usage

draw.ideogram(
  file_data,
  sizefile,
  output,
  directory = NULL,
  fileformat = "png",
  colours = colours.default,
  w = 8.5,
  h = 10,
  ps = 5
)

Value

An image file showing the ideogram

Arguments

file_data

Path to the syntenic blocks file

sizefile

Chromosome size file

output

output file name

directory

string containing file path to chosen directory to save image file

fileformat

output file format specified using fileformat = "pdf" (the default is "png")

colours

concatenated string of chromosome IDs and assigned colours if desired using the format colours = c("1" = "red", "2" = "blue", "3" = "green","X" = "grey") if the no colours are assigned default values will be used

w

width of output image using w = 8.5 (default)

h

height of output image using h = 10 (default)

ps

point size of output image using ps = 5 (default)

Details

This function draws pairwise synteny plots in chromosome painting style.

Inputs are tab separated files;

It requires as input:

1. File containing the syntenic blocks following this format: reference chromosome, reference start position, reference end position, target chromosome, target start position, target end position, orient, reference species identifier, target species identifier

2. 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. in this format: chromosome ID, chromosome length, species identifier

3. The desired output file name

Please separate files by tab and ensure any species identifiers used between length and alignment files are matching (same identifiers and caseing)

There are optional parameters for some customization of this function:

1. The format for saving the image i.e. png or pdf can be altered by inputting: fileformat = "pdf" (the default value is "png")

2. The colour of the ideograms can be altered by inputting a concatenated string of chromosome IDs with assigned colour values which can be found with R colour Pallette e.g. 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

3. The width of the image created can be changed by inputting: w = 8.5 (default)

4. The height of the image created can be changed by inputting: h = 10 (default)

5. The point size of the image created can be changed by inputting: ps = 5 (default)

6. The directory where the image file should be saved, as default the image is saved to temporary directory, change by inputting: directory = "path/to/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 chromosomes in the chromosome length file

Example: draw.ideogram("example_alignment_1.txt", "example_lengths.txt", "outputname", directory = "path/to/directory", fileformat = "pdf")

Examples

# Create objects containing file paths to external dataset
# (see vignette to follow examples with personal data)

length.file <- system.file("extdata", "example_lengths.txt", package = "syntenyPlotteR")
file1 <- system.file("extdata", "example_alignment_1.txt", package = "syntenyPlotteR")

# -----------------------------------------------------------------------------------

# Run draw.ideogram function
# To run example and save file to working directory
# add directory parameter and set working directory
# To run example with personal data see vignette

draw.ideogram(file1, length.file, "outputName", fileformat = "pdf")