jrplot: Jaccard vs. Ratio Segment Overlap Plots

In raim/segmenTools: Tools for Functional Genome Exploration

Jaccard vs. Ratio Segment Overlap Plots

Description

Generates a plot of Jaccard indices vs. query/target overlap Ratios, optionally decorated with threshold lines and counts.

Usage

jrplot(
  jaccard,
  ratio,
  symm = TRUE,
  nbin = 512,
  minn = 10,
  rlim = c(0, 2),
  jlim = c(0, 1.05),
  decorate = TRUE,
  xlb = expression("Jaccard Index" ~ J == I/U),
  ylb1 = expression(R == Q/T),
  ylb2 = expression(1/R == T/Q),
  yat = 0.5,
  j.thresh = 0.5,
  yd = 0.1,
  did = "",
  tot,
  ...
)

Arguments

jaccard	Jaccard Indices
ratio	query/target length ratio
symm	plot symmetric version, ie. for ratio>1 plot 1/ratio with inverted y-axis
nbin	nbin parameter for dense2d
minn	minimal number of available points to use dense2d, a conventional scatter plot (points) will be used if less than minn data are available
rlim	ratio (y-)axis limis
jlim	Jaccard (x-)axis limits
decorate	decorate the plot with Jaccard threshold and quartal numbers
xlb	x-axis label
ylb1	lower y-axis label for R<1 (Q<T) range
ylb2	upper x-axis label for R>1 (Q>T) range
yat	draw additional y-axis ticks at these positions (for R and 1/R)
j.thresh	Jaccard threshold, line will be drawn at this point, and counts reported for values below and above
yd	fraction of plot height to use for quartal number plot decoration
did	optional data ID to be used in the plot legend
tot	optional total number of targets to indicate non-overlapping targets in the plot legend
...	further arguments to dense2d or points

raim/segmenTools documentation built on April 25, 2024, 10:14 a.m.