plot_riparian: Make riparian plot using hits, not OGs

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

Make riparian plot using hits, not OGs

Description

plot_riparian Updated and more accurate version of plot_riparian

plot_riparian The main GENESPACE plotting routine, which generate braided river or 'riparian' plots.

riparian_engine underlying routines for plot_riparian, related to plotting and data parsing.

calc_curvePolygon from 2d coordinates, make a curve

round_rect from x-y coordinates, make a rounded rectangle

Usage

plot_riparian(
  gsParam,
  genomeIDs = gsParam$genomeIDs,
  refGenome = NULL,
  highlightBed = NULL,
  blk = NULL,
  backgroundColor = add_alpha("grey20", 0.5),
  pdfFile = NULL,
  useRegions = TRUE,
  labelTheseGenomes = gsParam$genomeIDs,
  useOrder = TRUE,
  gapProp = 0.005,
  chrFill = "white",
  scalePlotHeight = 1,
  scalePlotWidth = 1,
  minChrLen2plot = ifelse(useOrder, 100, 1e+05),
  braidAlpha = 0.5,
  scaleBraidGap = 0,
  reorderBySynteny = TRUE,
  howSquare = 0,
  customRefChrOrder = NULL,
  palette = gs_colors,
  chrLabFontSize = 5,
  chrExpand = 0.5,
  chrBorderCol = chrFill,
  syntenyWeight = 0.5,
  chrBorderLwd = 0.2,
  inversionColor = NULL,
  invertTheseChrs = NULL,
  forceRecalcBlocks = TRUE,
  chrLabFun = function(x) gsub("^0", "", gsub("chr|scaf|chromosome|scaffold|^lg|_", "",
    tolower(x))),
  xlabel = sprintf("Chromosomes scaled by %s", ifelse(useOrder, "gene rank order",
    "physical position")),
  scaleGapSize = 0.25,
  addThemes = NULL,
  verbose = FALSE,
  refChrOrdFun = function(x) frank(list(as.numeric(gsub("\\D+", "", x)), x),
    ties.method = "random")
)

riparian_engine(
  blk,
  bed,
  refGenome = NULL,
  genomeIDs = NULL,
  theseBlocksFirst = NULL,
  labelTheseGenomes = NULL,
  useOrder = TRUE,
  gapProp = 0.005,
  chrFill = "white",
  chrLabFontSize = 5,
  minChrLen2plot = ifelse(useOrder, 100, 1e+05),
  braidAlpha = 0.5,
  scaleBraidGap = 0,
  reorderBySynteny = TRUE,
  howSquare = 0,
  chrExpand = 0.5,
  chrBorderCol = NA,
  chrBorderLwd = 0,
  customRefChrOrder = NULL,
  palette = gs_colors,
  inversionColor = NULL,
  invertTheseChrs = NULL,
  syntenyWeight = 0.5,
  chrLabFun = function(x) gsub("^0", "", gsub("chr|scaf|chromosome|scaffold|^lg|_", "",
    tolower(x))),
  xlabel = sprintf("Chromosomes scaled by %s", ifelse(useOrder, "gene rank order",
    "physical position")),
  scaleGapSize = 0.25,
  addThemes = NULL,
  verbose = FALSE,
  refChrOrdFun = function(x) frank(list(as.numeric(gsub("\\D+", "", x)), x),
    ties.method = "random")
)

calc_curvePolygon(
  start1,
  end1 = NULL,
  start2,
  end2 = NULL,
  y1,
  y2,
  npts = 250,
  keepat = round(npts/20)
)

round_rect(
  xleft,
  ybottom,
  xright,
  ytop,
  plotWidth,
  plotHeight,
  xrange,
  yrange,
  npts = 50
)

Arguments

gsParam	A list of genespace parameters. This should be created by setup_genespace, but can be built manually. Must have the following elements: blast (file.path to the original orthofinder run), synteny ( file.path to the directory where syntenic results are stored), genomeIDs ( character vector of genomeIDs).
genomeIDs	character vector at least partially matching the genomeIDs in gsParam
refGenome	single character string specifying which genome is the ref
highlightBed	data.frame (or coercible to a data.frame, e.g. data.table) with four required columns: genome, chr, start, end ... these are the bp coordinates of the regions of interest. Can also include a column "color" with the desired color to plot for that particular regions. This can be used to color chromosomes in polyploid references.
blk	data.table of block coordinates
backgroundColor	character or integer coercible to an R color. Only used if highlightBed is also specified. This is background to show all blocks across references. If the full background is not desired, can be set to NULL or NA. In which case the plot will ONLY contain the regions specified in highlightBed.
pdfFile	file.path to the pdf device to store the file
useRegions	logical, should regions or smaller blocks be plotted?
labelTheseGenomes	character string of genomes that have labeled chrs
useOrder	logical, should gene rank order be used in lieu of physical positions?
gapProp	numeric (0-1) specifying the proportional size of gaps relative to the length of the largest genome
chrFill	character or integer coercible to an R color for the interior fill of the chromosome regions
scalePlotHeight	numeric, scaling factor for plot height Larger values make taller plots
scalePlotWidth	numeric, scaling factor for plot width. Larger values make wider plots
minChrLen2plot	replaces previous minSize2plot. Minimum size in the scale plotted (order if useOrder = TRUE, bp if useOrder = FALSE)
braidAlpha	numeric (0-1) specifying the transparency of the braids
scaleBraidGap	integer specifying how much of a gap should exist between the center of the chromosome labels (y position) and the begining of the braid polygons. 0 = no gap between braids, 1 = gap equal to the vertical size of the chromosome polygons so that the braids start and the bottom/top of the chromosome polygons. Scales linearly form there.
reorderBySynteny	logical, should chromosomes be re-ordered by synteny?
howSquare	numeric 0-inf, specifying how square the rounded rectangles should be. 0 = no straight sections. Inf = no rounded sections
customRefChrOrder	character vector with the order of chromosomes in the reference genome
palette	function coercible to an R color palette
chrLabFontSize	size in points for the chromosome labels
chrExpand	numeric giving the expansion of the chromosome polygons surrounding the chromosome labels.
chrBorderCol	color of the chromosome polygon borders
syntenyWeight	currently can be 0,.5,1. 0 is equivalent to reorderBySynteny = FALSE. 1 is the previous behavior (synteny is fully respected). Anything between 0
chrBorderLwd	line width of the chromosome polygon borders
inversionColor	= NULL,
invertTheseChrs	data.table with two columns, genome and chr containing the lists of genomes and chromosomes that should be inverted in the plot. Not currently implemented.
forceRecalcBlocks	logical, should the phased blocks be re-calculated even if there is a phased block file.
chrLabFun	function to parse chr IDs to make them more readible
xlabel	label for the x axis of the plot
scaleGapSize	numeric 0-1, specifying the gap scaling level, where 0 means all gaps are the same size regardless of genome size. 1 means that the genomes sizes are all nearly the same and smaller genomes have larger gaps.
addThemes	ggplot2 themes to add to the riparian plot
verbose	logical, should updates be printed to the console?
refChrOrdFun	function, to re-order reference chromosomes
bed	data.table with combined bed file
theseBlocksFirst	internal parameter specifying which blocks should be plotted first
start1	numeric, start postion of the first block
end1	numeric, end postion of the first block
start2	numeric, start postion of the second block
end2	numeric, end postion of the second block
y1	numeric, bottom postion of the block
y2	numeric, top postion of the block
npts	integer, the number of points to use in the curve.
keepat	integer, the grid size of points to keep
xleft	numeric, left position of rounded rectangle
ybottom	numeric, bottom position of rounded rectangle
xright	numeric, right position of rounded rectangle
ytop	numeric, top position of rounded rectangle
plotWidth	numeric, width of the plot
plotHeight	numeric, height of the plot
xrange	numeric, x range of data
yrange	numeric, y range of the data

Details

By default, acts directly on the reference-phased syntenic block coordinates generated by integrate_synteny(). Uses these positions to generate linear coordinates for block breakpoints and colors these by the reference genome chromosomes.

Examples

## Not run: 
# see vignette dedicated to plot_riparian, coming soon.

## End(Not run)

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