bayesinfo_pairwise: Import and summarize results from analyses set by the...

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

Import and summarize results from analyses set by the galaxscrip_pairwise function.

Description

Import and summarize results from analyses set by the galaxscrip_pairwise function.

Usage

bayesinfo_pairwise(ids = ids, runs = 2, profile = F, cluster = T)

Arguments

ids	data.frame or list, if profile = 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 should be a list of profiles organized as indicated in the examples.
profile	logical, if TRUE specify that the input in ids is a list of profiles to query, organized as indicated in the examples.
cluster	logical. If TRUE plots the resultant dissonance clustering dendrogram.

Value

A dissimilarity matrix based on values of phylogenetic dissonance obtained from all pairwise comparisons between anatomical data subsets.

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 all pairwise comparisons of terms #
pp1 <- bayesinfo_pairwise(ids = ID, runs = 2, profile = F, cluster = T)

# 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")

# Import and visualize results from all pairwise comparisons of terms in user defined profiles #
tt1 <- bayesinfo_pairwise(ids = tags, runs = 2, profile = T, cluster = T)

# 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))))

# Import and visualize results from all pairwise comparisons of terms #
pp2 <- bayesinfo_pairwise(ids = ID, runs = 2, profile = F, cluster = T)

# 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")

# Import and visualize results from all pairwise comparisons of terms in user defined profiles #
tt2 <- bayesinfo_pairwise(ids = tags, runs = 2, profile = T, cluster = T)

## End(Not run)

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