ontostructure: Gets the ontology hierarchical structure represented as a...

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

Gets the ontology hierarchical structure represented as a semantic similarity or dissonance dendrogram #

Description

Gets the ontology hierarchical structure represented as a semantic similarity or dissonance dendrogram #

Usage

ontostructure(
  ids = ids,
  dsm = dsm,
  similarity = "jaccard",
  manual = F,
  plot = F
)

Arguments

ids	data.frame, if manual = F, ids should be a data.frame providing 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). Otherwise, ids can be ommited.
dsm	matrix, if manual = T, dsm should be a dissimilarity matrix obtained from the function bayesinfo_pairwise. Otherwise, dsm can be ommited.
similarity	character, the metric chosen to produce a semantic similarity dendrogram. Default is set to "jaccard". This option is the only one currently available. Future developments will allow to use other metrics such as "resnik". This options is available only if Uberon ontology terms are employed since it uses dependencies from rphenoscape to build a semantic similarity dendrogram as a representation of the ontology structure.
manual	logical, if TRUE specify that a dissimilarity matrix based on phylogenetic dissonance will be provide to produce a dendrogram. Otherwise, a dendrogram will be produced using a dissimilarity matrix based on the semantic similarity metric chosen.
plot	logical, If TRUE plots the resultant semantic similarity or dissonance dendrogram.

Value

A list with all terms subtended by each internal node of the semantic similarity or dissonance dendrogram.

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))))

# Import and visualize results from pairwise comparisons of terms #
pp <- bayesinfo_pairwise(ids = ID, runs = 2, profile = F, cluster = T)

# Get hierarchical structure based on dissonance dendrogram #
hstruc1 <- ontostructure(dsm = pp, manual = T, plot = F)

# 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))))

# Get hierarchical structure based on semantic similarity dendrogram #
hstruc2 <- ontostructure(ids = ID, manual = F, plot = F, similarity = "jaccard")

## End(Not run)

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