TIMBR.plot.circos: Circos Plot of Pairwise Partition Probabilities from TIMBR...

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

Description

Plots the probability that each pair of haplotypes is partitioned together on a circos plot; includes heatmap of relative effect sizes when using TIMBR results

Usage

TIMBR.plot.circos(
  TIMBR.object,
  file.path = NULL,
  plot.width = 480,
  plot.height = 480,
  post.summary = "mean",
  colors = c("blue", "white", "red"),
  fixed.order = NULL
)

Arguments

TIMBR.object	results object from the TIMBR function; or prior.M object of "list" type
file.path	an optional file path for saving the plot as a PNG
plot.width	PNG plot width
plot.height	PNG plot height
post.summary	posterior summary for relative effect size; select from c("mean", "median", "mode")
colors	colors for heatmap of relative effect sizes
fixed.order	vector of letters to specify plot order

Value

circos plot of pairwise partition probabilities

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 partition probabilities
TIMBR.plot.circos(results)

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