plot_bayesinfo: Plot Bayesian phylogenetic information or dissonance values...

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

Plot Bayesian phylogenetic information or dissonance values at tips or internal nodes of a reference semantic similarity or dissonance dendrogram.

Description

Plot Bayesian phylogenetic information or dissonance values at tips or internal nodes of a reference semantic similarity or dissonance dendrogram.

Usage

plot_bayesinfo(
  phy = phy,
  struc = struc,
  bpi = bpi,
  stdz = c(1, 1),
  plot = T,
  tcex = 0.5,
  type = "information",
  mode = "internal"
)

Arguments

phy	phylo or hclust, a reference semantic similarity or dissonance dendrogram.
struc	list, the output from the ontostructure function.
bpi	matrix or list, information teory metrics to be ploted onto the reference dendrogram. If mode = "terminal", a matrix with values of posterior coverage, Bayesian phylogenetic information, and phylogenetic dissonance as the output of the bayesinfo function. If mode = "internal", a list of matrices with values of posterior coverage, Bayesian phylogenetic information, and phylogenetic dissonance for each internal node of the semantic similarity or dissonance dendrogram as the output of the bayesinfo_structure function.
stdz	numeric, amount to standardize values Bayesian phylogenetic information and dissonance. If mode = "terminal", stdz should be a single number. If mode = "internal", stdz should be a pair of numbers. Default is set to c(1,1).
plot	logical, if TRUE plots values of Bayesian phylogenetic information or dissonance at internal nodes when mode = "internal". Otherwise, only returns a matrix with mean values between mcmc runs of Bayesian phylogenetic information and dissonance for all internal nodes of the reference dendrogram.
tcex	numeric, sets the font size for tip labels in the dendrogram. Default is set to 0.5.
type	character, sets the type of information theory metrics to plot. If type = "information", plots Bayesian phylogenetic information. If type = "dissonance", plots phylogenetic dissonance. Defaut is set to "information".
mode	character, sets whether information theory metrics should be plotted for terminals or internal nodes of the reference dendrogram. If mode = "terminal", plots the chosen IT metric for individual anatomical data subsets defined by the ontology terms at tips. If mode = "internal", plots the chosen IT metric for comparisons among anatomical data subsets subtended by the internal nodes indicated in the reference dendrogram.

Value

A matrix with mean values between mcmc runs of Bayesian phylogenetic information and dissonance for all internal nodes of the reference dendrogram if mode = "internal", otherwise only plots the dendrogram with the chosen IT metrics (i.e., information or dissonance) and mode (i.e., terminal or internal).

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 a reference dendrogram based on phylogenetic dissonance #
phy1 <- hclust(as.dist(pp))

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

# Import results from comparisons among terms according to dissonance dendrogram #
struc1 <- bayesinfo_structure(struc = hstruc1, runs = 2)

# Import and summarize results from comparisons among runs for all terms #
runs1 <- bayesinfo(ids = ID) 

# Plot dendrogram with information of individual anatomical data subsets at tips # 
plot_bayesinfo(phy = phy1, bpi = runs1, stdz = 1, mode = "terminal")

# Plot dendrogram with information of among anatomical data subsets at internal nodes # 
plot_bayesinfo(phy = phy1, struc = hstruc1, bpi = struc1, stdz = c(10, 10), mode = "internal", type = "information")

# Plot dendrogram with dissonance of among anatomical data subsets at internal nodes #
plot_bayesinfo(phy = phy1, struc = hstruc1, bpi = struc1, stdz = c(10, 10), mode = "internal", type = "dissonance")

# 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")

# Import results from comparisons among terms according to ontology structure #
struc2 <- bayesinfo_structure(struc = hstruc2, runs = 2)

# Build a semantic similarity dendrogram"] #
sm <- paste0("http://purl.obolibrary.org/obo/", gsub(unique(ID[,2]), pattern = ":", replacement = "_"))
sm <- rphenoscape:::jaccard_similarity(terms = sm, .colnames = c("label"))
phy2 <- hclust(as.dist(1 - sm))

# Import and summarize results from comparisons among runs for all terms #
runs2 <- bayesinfo(ids = ID) 

# Plot dendrogram with information of individual anatomical data subsets at tips # 
plot_bayesinfo(phy = phy2, bpi = runs2, stdz = 1, mode = "terminal")

# Plot dendrogram with information of among anatomical data subsets at internal nodes # 
plot_bayesinfo(phy = phy2, struc = hstruc2, bpi = struc2, stdz = c(10, 10), mode = "internal", type = "information")

# Plot dendrogram with dissonance of among anatomical data subsets at internal nodes #
plot_bayesinfo(phy = phy2, struc = hstruc2, bpi = struc2, stdz = c(10, 10), mode = "internal", type = "dissonance")

## End(Not run)

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