plot_outlier_ideogram: Plot an Ideogram for BGC Outlier Genes

In btmartin721/ClineHelpR: Parses and Plots BGC and INTROGRESS Output

Plot an Ideogram for BGC Outlier Genes

Description

For this function to work, you must have a closely related reference genome and must run minimap2 externally (tested with v2.17). minimap2 maps assembly scaffolds to a reference genome. This includes all the unplaced assembly scaffolds as well as the transcriptome combined into one assembly fasta file. minimap2 should be run with the –cs and -N 100 options with default PAF file output format. You will need to adjust the asm value to suit how closely related your reference genome is (i.e. sequence divergence). See the minimap2 documentation for more info: https://github.com/lh3/minimap2. Then, you need to run PAFScaff on the PAF file output from minimap2 (https://github.com/slimsuite/pafscaff). PAFScaff parses the minimap2 output and improves the mapping. The scaffolds.tdt.file value is the *.scaffolds.tdt output file from PAFScaff, and you need it for this function. Ref chromosomes should be named integers in PAFScaff (1, 2, etc.). This funtion also depends on previous output from get_bgc_outliers() and join_bgc_gff(). See ?get_bgc_outliers and ?join_bgc_gff. You should run BGC and get_bgc_outliers() separately for both transcriptome-aligned data and all other scaffolded loci. Then run join_bgc_gff() on only the transcriptome-aligned data. Both are required as input to make the ideograms. You can also see https://cran.r-project.org/web/packages/RIdeogram/index.html for more info on plotting the RIdeograms.

Usage

plot_outlier_ideogram(
  prefix,
  outliers.genes,
  outliers.full.scaffolds,
  pafInfo,
  plotDIR = "./plots",
  both.outlier.tests = FALSE,
  both.outlier.tests.genes = FALSE,
  overlap.zero = TRUE,
  overlap.zero.genes = TRUE,
  qn.interval = TRUE,
  qn.interval.genes = TRUE,
  missing.chrs = NULL,
  miss.chr.length = NULL,
  gene.size = 5e+05,
  other.size = 1e+05,
  convert_svg = "pdf",
  colorset1 = c("#4575b4", "#ffffbf", "#d73027"),
  colorset2 = c("#4575b4", "#ffffbf", "#d73027"),
  chrnum.prefix = NULL,
  genes.only = FALSE,
  linked.only = FALSE
)

Arguments

prefix	Prefix for output files
outliers.full.scaffolds	List containing outlier data from get_bgc_outliers(). See ?get_bgc_outliers. This must be loci aligned to full scaffolds
pafInfo	Path to *.scaffolds.tdt file output from PAFScaff
plotDIR	Directory to save output plots
both.outlier.tests	Boolean; If TRUE, scaffold outliers must meet both the overlap.zero and qn.interval criteria
both.outlier.tests.genes	Boolean; If TRUE, gene outliers must meet both the overlap.zero.genes and qn.interval.genes criteria
overlap.zero	Boolean; If TRUE, scaffold outliers are SNPs whose credible interval does not contain zero
overlap.zero.genes	Boolean; If TRUE, gene outliers are SNPs whose credible interval does not contain zero
qn.interval	Boolean; If TRUE, scaffold outliers fall outside the quantile interval qn/2 and 1-qn/2
qn.interval.genes	Boolean; If TRUE, gene outliers fall outside the quantile interval qn/2 and 1-qn/2
missing.chrs	If specified, must be character vector of missing chromosome names. Chromosome numbers should be prefixed with "chr". I.e., c("chr3", "chr6"). If some chromosomes don't get plotted, use this option
gene.size	Adjust the size for each outlier transcriptome gene on the ideogram. If the loci appear too small or large on the ideogram, adjust just this parameter
other.size	Adjust the size for each outlier scaffold gene on the ideogram
convert_svg	Device to convert SVG output plot. Default is pdf, but you can use png or other commonly used devices
colorset1	Vector of colors for RIdeogram alpha heatmap. Default is the same as the RIdeogram defaults
colorset2	Vector of colors for RIdeogram beta heatmap. Default is the same as the RIdeogram defaults
chrnum.prefix	Prefix for chromosome numbers on ideaogram plot
genes.only	Boolean; If TRUE, only include known genes on ideogram
linked.only	Boolean; If TRUE, only include non-genes on ideogram
outliers.genes.annotated	List containing gene outlier data from get_bgc_outliers(). See ?get_bgc_outliers. This must be outliers from a transcriptome alignment
missing.chr.length	Vector of integer lengths (in bp) of missing chromosomes. Must also be specified if missing.chrs is used. Vector must also be the same length as missing.chrs

Details

Function to plot outlier BGC loci as heatmaps on chromosome ideograms.

Value

Data.frame containing reference info for gene outliers.

Examples

plot_outlier_ideogram(prefix = "population1",
                      outliers.genes.annotated = outliers.genes.annotated,
                      outliers.full.scaffolds = outliers.full.scaffolds,
                      pafInfo = "./population1.scaffolds.tdt",
                      plotDIR = "./plots",
                      both.outlier.tests = TRUE,
                      missing.chrs = c("chr11", "chr21", "chr25"),
                      miss.chr.length = c(4997863, 1374423, 1060959),
                      gene.size = 1e6,
                      other.size = 5e5,
                      convert_svg = "png",
                      colorset1 = c("#4575b4", "#ffffbf", "#d73027"),
                      colorset2 = c("#fc8d59", "#ffffbf", "#91bfdb")

btmartin721/ClineHelpR documentation built on Oct. 15, 2024, 5:05 a.m.