calc_tree: Generate phylogenetic-like clustering trees.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Generate phylogenetic-like clustering trees.

Description

Generate dendritic trees in the style of a phylogenetic tree for individuals or groups of individuals from snpR data. Note that this function is not overwrite safe.

Usage

calc_tree(
  x,
  facets = NULL,
  distance_method = "Edwards",
  interpolate = "bernoulli",
  tree_method = "nj",
  root = FALSE,
  boot = FALSE,
  boot_par = FALSE,
  update_bib = FALSE
)

Arguments

x	snpRdata object.
facets	character or NULL, default NULL. Facets for which to calculate genetic distances, as described in Facets_in_snpR. If snp or base level facets are requested, distances will be between individuals. Otherwise, distances will be between the levels of the sample facets.
distance_method	character, default "Edwards". Name of the method to use. Options: Edwards Angular distance as described in Edwards 1971. See calc_genetic_distances.
interpolate	character, default "bernoulli". Missing data interpolation method, solely for individual/individual distances. Options detailed in documentation for format_snps.
tree_method	character, default nj. Method by which the tree is constructed from genetic distances. Options: nj Neighbor-joining trees, via nj. bionj BIONJ trees, according to Gascuel 1997, via bionj. upgma UPGMA trees, via hclust.
root	character or FALSE, default FALSE. A vector containing the requested roots for each facet. Roots are specified by a string matching either the individual sample or sample facet level by which to root. If FALSE for a given facet, trees will be unrooted. Note that all UPGMA trees are automatically rooted, so this argument is ignored for that tree type.
boot	numeric or FALSE, default FALSE. The number of bootstraps to do for each facet. See details.
boot_par	numeric or FALSE, default FALSE. If a number, bootstraps will be processed in parallel using the supplied number of cores.
update_bib	character or FALSE, default FALSE. If a file path to an existing .bib library or to a valid path for a new one, will update or create a .bib file including any new citations for methods used. Useful given that this function does not return a snpRdata object, so a citations cannot be used to fetch references.

Details

Trees are generated via the nj or bionj ape package for nj or bionj trees. Plots of the resulting trees can be produced using other plotting tools, such as the geom_tree function from ggtree. These are not produced automatically because ggtree can have unexpected outputs, but the process is straightforward and examples are provided in the examples section of this documentation. For more information, see the documentation for those functions and packages.

Bootstraps are conducted by re-sampling SNPs with replacement, according to Felsenstein (1985). If no snp level facets are provides, loci are resampled without restraint. If a snp level facet is provided, loci are only resampled within the levels of that facet (e.g. within chromosomes).

The genetic distances used to make the trees are calculated using calc_genetic_distances. If a sample facet is used, that function uses code derived from adegenet. Please cite them and the actual method (e.g. Edwards, A. W. F. (1971)) alongside the tree-building approach.

Bootstrapping is done via the boot.phylo function in the ape package, and as such does not support parallel runs on Windows machines.

Value

A nested, named list containing plots, trees, and bootstraps for each facet and facet level.

Author(s)

William Hemstrom

References

Felsenstein, J. (1985). Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39(4), 783–791. https://doi.org/10.2307/2408678

Gascuel, O. (1997).BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14(7), 685–695. https://doi.org/10.1093/oxfordjournals.molbev.a025808

Paradis, E., Claude, J. and Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289–290.

Examples

# Calculate nj trees for the base facet, each chromosome, 
# and for each population.

# note: some versions of ggtree/ggplot2 give an error relating to unable
# to use 'fortify()' when attempting to plot that is potentially due to
# ape masking something when loading snpR. Saving the tree object as
# a .RDS object with 'saveRDS()', restarting R, loading the object in,
# then plotting without loading snpR seems to fix the issue.

## Not run: 

# make the trees
tp <- plot_tree(stickSNPs, c(".base", "pop", "chr"), 
                root = c(FALSE, "PAL", FALSE))

# plot using the ggtree package. Not done internally due to unpredictable
# ggtree behavior
library(ggtree)
ggplot(tp$pop$.base, aes(x, y)) + 
  geom_tree() +
  geom_tiplab() + theme_tree()

# Calculate bionj trees for pop with bootstrapping
tp <- plot_tree(stickSNPs, "pop", root = "PAL", boot = 5)
## plot
ggplot(tp$pop$.base, aes(x, y)) + 
  geom_tree() +
  geom_tiplab() + theme_tree() +
  geom_text2(ggplot2::aes(subset = !isTip, label = label),
                          hjust = -.3)

## End(Not run)

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.