ontobayes_profiles: Builds MrBayes NEXUS files for subsets of characters...

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

Builds MrBayes NEXUS files for subsets of characters annotated with ontology anatomy terms based on a chosen profile of terms.

Description

Builds MrBayes NEXUS files for subsets of characters annotated with ontology anatomy terms based on a chosen profile of terms.

Usage

ontobayes_profiles(
  tags = tags,
  ids = ids,
  manual = T,
  relations = c("part_of", "is_a"),
  ontology = "data/ontology.obo",
  dataset = "data/matrix.nex",
  outgroup = "outroup_taxon",
  rates = "gamma",
  coding = "all",
  ratepr = "fixed",
  brlenspr = "Unconstrained:Exp(10)",
  gen = 1e+06,
  runs = 2,
  chains = 4,
  freq = 1000
)

Arguments

tags	list, profiles with anatomy ontology terms to query. The list of profiles should be organized as indicated in the examples.
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).
manual	logical, if TRUE specify that an ontology file (OBO format) is provided by the user. This option is the only one currently available. Future developments will allow to access Uberon ontology directly using rphenoscape dependencies.
relations	character, set the types of ontological relations to use. Default is set to c("part_of", "is_a").
ontology	character, name of the OBO file with the ontology.
dataset	character, name of the NEXUS file with the character matrix to be read.
outgroup	character, name of the outgroup taxon.
rates	character, sets the model of among-character rate variation in the MrBayes commands block. Default is set to "equal".
coding	character, sets the coding bias in the MrBayes commands block. Default is set to "all".
ratepr	character, sets the character specific or partition specific rates model in the MrBayes commands clock. Default is set to "fixed".
brlenspr	character, sets the branch lengths prior in the MrBayes commands block. Deafault is set to "Unconstrained:Exp(10)".
gen	integer, sets the number of generations of mcmc in the MrBayes commands block. Default is set to 1000000.
runs	integer, sets the number of independent runs of mcmc in the MrBayes commands block. Default is set to 2.
chains	integer, sets the number of chains for each run in the MrBayes commands block. Default is set to 4.
freq	integer, sets the sampling frequency for the mcmc in the MrBayes commands block. Default is set to 1000.

Value

Individual NEXUS files for each subset of characters annotated with ontology anatomy terms. The files will be organized in individual subfolders named according to each profile inside the folder NEXUS.

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))))

# List of profiles with terms to query #
tags <- list(
  c("HAO:0000506", "HAO:0000513", "HAO:0000453"),
  c("HAO:0000234", "HAO:0001003"),
  c("HAO:0000874", "HAO:0000583", "HAO:0000630"))

# Set profile names and terms #
names(tags) <- c("mouthparts_profile1", "head_profile2", "mesosoma_profile3")
names(tags[[1]]) <- c("mandible", "maxilla", "labium")
names(tags[[2]]) <- c("cranium", "tentorium")
names(tags[[3]]) <- c("prothorax", "mesothorax", "metathorax")

# Create MrBayes files #
ontobayes_profiles(tags = tags, ids = ID, manual = T, relations = c("BFO:0000050", "is_a"), ontology = "data/HAO.obo", 
dataset = "data/matrix1.nex", outgroup = "sp1", rates = "gamma", coding = "variable", 
gen = 1000000, runs = 2, chains = 4)

# 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))))

# List of profiles with terms to query #
tags <- list(
  c("UBERON_0002244", "UBERON_0002397", "UBERON_0004742"),
  c("UBERON_2000658", "UBERON_2000488"),
  c("UBERON_0000151", "UBERON_0000152", "UBERON_0003097"))

# Set profile names and terms #
names(tags) <- c("jaw_profile1", "pharynx_profile2", "fins_profile3")
names(tags[[1]]) <- c("premaxilla", "maxilla", "dentary")
names(tags[[2]]) <- c("epibranchial_bone", "ceratobranchial_bone")
names(tags[[3]]) <- c("pectoral_fin", "pelvic_fin", "dorsal_fin")

# Create MrBayes files #
ontobayes_profiles(tags = tags, ids = ID, manual = T, relations = c("part_of", "is_a"), ontology = "data/UBERON.obo", 
dataset = "data/matrix2.nex", outgroup = "sp1", rates = "gamma", coding = "variable", 
gen = 1000000, runs = 2, chains = 4)

## End(Not run)

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