plot_treedistr: A wraper function to visualize the posterior distribution of...

In diegosasso/ontobayes: Ontology-aware Bayesian Phylogenetic Information Analysis of Morphological Data

A wraper function to visualize the posterior distribution of tree topologies for data subsets based on selected anatomy ontology terms.

Description

This wraper uses the functions makeplot.topology and makeplot.treespace from package rwty (Warren et al. 2017) to provide an easy visualization of the tree space for the posterior distributions of data subsets defined by selected anatomy ontology terms.

Usage

plot_treedistr(
  ids = ids,
  tags = tags,
  burnin = 251,
  res = 100,
  tdist = "PD",
  mode = "distribution"
)

Arguments

ids	data.frame, matches between characters and anatomical entities. The first column should provide character ids in the same order as presented in the character matrix. The second column should provide the respective ontology ids referring to the anatomical entities. The third column should provide the respective ontology terms referring to the anatomical entities. See examples provided in the data folder (data1.csv and data2.csv).
tags	character, a vector with the names of the anatomical data subsets to produce the tree spaces. Names should match those in the third column of the ids data.frame.
burnin	integer, the absolute number of trees as the burn-in used in the mcmc. Default is set to 251.
res	integer, if mode = "densitymap", sets the number of trees to sample from the posterior distribution.
tdist	character, sets the type of tree distance metric to use. The options are "PD" for path distance or "RB" for Robinson Foulds distance. Default is set to "PD". See the help of makeplot.topology function in the rwty package for more details.
mode	character, sets the type of visualization to use. The options are "distribution" to use the tree distance trace plot from the makeplot.treespace function of rwty or "densitymap" to use the density map plot from the makeplot.treespace function of rwty. See the help of makeplot.topology and makeplot.treespace functions in the rwty package for more details.

Value

A tree trace plot or a density map plot for data subsets based on selected anatomy ontology terms.

Examples

## Not run: 
# HAO example #
# Create ID object #
ID <- as.data.frame(cbind(paste0("C", 1:40),
c(rep("HAO:0000506",5), rep("HAO:0000513",5), rep("HAO:0000453",5), rep("HAO:0000234",5), 
rep("HAO:0001003",5), rep("HAO:0000874",5), rep("HAO:0000583",5), rep("HAO:0000630",5)),
c(rep("mandible",5), rep("maxilla",5), rep("labium",5), rep("cranium",5)
, rep("tentorium",5), rep("prothorax",5), rep("mesothorax",5), rep("metathorax",5))))

# Choose some terms annotated to characters in the matrix #
tg1 <- c("mandible", "maxilla")

# Plot tree trace plot from RWTY package #
plot_treedistr(ids = ID, tags = tg1, burnin = 251, res = 500, tdist = "PD", mode = "distribution")

# UBERON example #
# Create ID object #
ID <- as.data.frame(cbind(paste0("C", 1:40),
c(rep("UBERON_0002244",5), rep("UBERON_0002397",5), rep("UBERON_0004742",5), rep("UBERON_2000658",5), 
rep("UBERON_2000488",5), rep("UBERON_0000151",5), rep("UBERON_0000152",5), rep("UBERON_0003097",5)),
c(rep("premaxilla",5), rep("maxilla",5), rep("dentary",5), rep("epibranchial bone",5)
, rep("ceratobranchial bone",5), rep("pectoral fin",5), rep("pelvic fin",5), rep("dorsal fin",5))))

# Choose some terms annotated to characters in the matrix #
tg2 <- c("premaxilla", "maxilla")

# Plot tree trace plot from RWTY package #
plot_treedistr(ids = ID, tags = tg2, burnin = 251, res = 500, tdist = "PD", mode = "distribution")

## End(Not run)

diegosasso/ontobayes documentation built on May 3, 2022, 10:23 p.m.