plot_2genomes: Comparative genome structure plots

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

Comparative genome structure plots

Description

plot_2genomes Single function to find synteny between two genomes and plot the density of genes and repeats along with syntenic links

Usage

plot_2genomes(
  genomeIDs,
  faFiles,
  wd,
  geneGffFiles,
  repeatGffFiles,
  minChrSize = 1e+06,
  verbose = TRUE,
  kmers = NULL,
  nCores = 1,
  kmerMisMatch = 0,
  slidingwindowSize = 1e+06,
  slidingwindowStep = 1e+05,
  plotGapSize = 0.1,
  repeatClassColumnName = "class",
  repeatGrep1 = "Gypsy",
  repeatGrep2 = "Copia",
  cdsGrep = "CDS",
  transcriptGrep = "mRNA",
  plotCols = NULL,
  plotTheme = NULL,
  overwrite = FALSE,
  pdfFile = NULL,
  returnSourceData = FALSE,
  forceCleanWindows = FALSE,
  ...
)

Arguments

genomeIDs	character vector specifying the genome IDs
faFiles	character vector coercible to file paths specifying the locations of the fasta assembly files
wd	character string coercible to file path where the results should be stored
geneGffFiles	character vector coercible to file paths specifying the locations of the gene gff3 annotation files
repeatGffFiles	character vector coercible to file paths specifying the locations of the repeatmasker (or similar) gff3 annotation files
minChrSize	integer specifying the minimum chromosome size to use
verbose	logical specifying whether updates should be printed to the console
kmers	character specifying kmers that should be classified, defualt is to not plot kmer density
nCores	integer specifying the number of parallel processes to run
kmerMisMatch	integer specifying the number of mismatches allowed when search for kmer matches
slidingwindowSize	integer specifying the sliding window size
slidingwindowStep	integer specifying the step between windows
plotGapSize	numeric (0-1) specifying the size of gaps between the largest genomes chromosomes as a fraction of the total genome size
repeatClassColumnName	character specifying which column should be used to grep for repeat classes
repeatGrep1	character specifying the string to grep for the first repeat density
repeatGrep2	character specifying the string to grep for the second repeat density
cdsGrep	character specifying the string to grep for CDS in the gene gff3 annotation file
transcriptGrep	character specifying the string to grep for transcript in the gene gff3 annotation file
plotCols	character vector specifying the plot colors
plotTheme	ggplot2 theme to add to the plot
overwrite	logical specifying whether results should be overwritted
pdfFile	character string coercible to a file path where the plot should be written
returnSourceData	logical, should source data be returned
forceCleanWindows	logical, should clean windows output be overwritten?
...	additional arguments passed to clean_windows

Details

Coming soon

Value

A plot, written to file.

Examples

## Not run: 
# coming soon

## End(Not run)

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.