TIMBR.plot.haplotypes: Plot Haplotype Effects from TIMBR Output

In wesleycrouse/TIMBR: Tree-based Inference of Multiallelism via Bayesian Regression

Description

Plots posterior haplotype effect densities from TIMBR output

Usage

TIMBR.plot.haplotypes(
  TIMBR.output,
  colors = NULL,
  file.path = NULL,
  plot.width = 960,
  plot.height = 480,
  TIMBR.output.bkgrd = NULL,
  colors.bkgrd = NULL,
  transparency = c(0.7, 0.4),
  y.lab = "Haplotype",
  hap.labels = NULL,
  x.lim = NULL,
  x.lab = NULL,
  cex.axis = 1,
  cex.lab = 1,
  cex.main = 1,
  font.main = 2
)

Arguments

TIMBR.output	results object from the TIMBR function
colors	an optional vector of colors for each haplotype density
file.path	an optional file path for saving the plot as a PNG
plot.width	PNG plot width
plot.height	PNG plot height
TIMBR.output.bkgrd	optional second results object for background plot
colors.bkgrd	optional colors for background plot
transparency	optional vector of transparencies for foreground and background plots, ignored if second results object is not specified
y.lab	graphical parameter for plot
hap.labels	optional labels for haplotypes
x.lim	optional limits for x axis
x.lab	optional label for x axis
cex.axis	graphical parameter for plot
cex.lab	graphical parameter for plot
cex.main	graphical parameter for plot
font.main	graphical parameter for plot

Value

plot of the posterior haplotype effect densities

Examples

#example data
data(mcv.data)
str(mcv.data)

#call TIMBR using CRP
results <- TIMBR(mcv.data$y, mcv.data$prior.D, mcv.data$prior.M$crp)

#plot haplotype effects
TIMBR.plot.haplotypes(results)

wesleycrouse/TIMBR documentation built on Feb. 19, 2021, 7:31 a.m.