plot_hits: plot hits as a xy dotplot

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

plot hits as a xy dotplot

Description

plot_hits routines to make visually appealing dotplots

plot_hits The pipeline to plot syntenic hits in parallel

ggdotplot ggplot2 integrated graphics to produce dotplots

gghits ggplot2 integrated graphics to produce dotplots

Usage

plot_hits(
  gsParam,
  verbose = TRUE,
  type,
  dotsPerIn = 256,
  quantileThresh = 0.5,
  plotSize = 12,
  minScore = 50
)

ggdotplot(
  hits,
  type,
  outDir = NULL,
  minGenes2plot = 100,
  appendName = "synHits",
  dotsPerIn = 256,
  quantileThresh = 0.5,
  plotSize = 12,
  minScore = 50,
  maxFacets = 10000,
  verbose = is.null(outDir)
)

gghits(
  hits,
  colorByBlks = TRUE,
  alpha = ifelse(colorByBlks, 1, 0.25),
  useOrder = TRUE,
  minScore = 0,
  minGenes2plot = 0
)

Arguments

gsParam	A list of genespace parameters. This should be created by init_genespace.
verbose	logical, should updates be printed to the console?
type	character string of "all", "raw", or "syntenic" specifying which type of dotplot to generate.
dotsPerIn	integer specifying how fine-scaled the heatmap is
quantileThresh	integer specifying the top quantile to be thresholded
plotSize	numeric smalled dimension of the plot
minScore	numeric, the minimum scoring hit to plot
hits	data.table containg hits. See read_allBlast.
outDir	file.path where pdf should be written
minGenes2plot	integer, the minimum number of hits to plot a chromosome combination. If called, plot_hits returns its own arguments.
appendName	character with text to append to the file name
maxFacets	integer the maximum number of facets to plot (doesn't plot for genomes with lots of small chrs/scaffolds)
colorByBlks	logical, should blocks be colored?
alpha	numeric [0-1], specifying the transparency of the points
useOrder	logical, should gene order or bp position be used?

Details

Dotplots here aggregate across proximate positions to reduce file size, especially for very large genomes. XY positions are always in gene-rank order positions. Graphics are built with ggplot2.

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