plotSigTree: Function to plot the phylogenetic tree in R with branches...

In SigTree: Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

Description

plotSigTree takes tree and unsorted.pvalues and computes p-values for each branch (family of tips) and colors the corresponding descendant branches. It computes the p-values based on arguments involving p-value adjustment (for multiple hypothesis testing) and either Hartung's, Stouffer's, or Fisher's p-value combination method. There are arguments that allow for the customization of the p-value cutoff ranges as well as the colors to be used in the coloring of the branches.

Usage

plotSigTree(tree, unsorted.pvalues, adjust=TRUE, side=1, 
	method="hommel", p.cutoffs=ifelse(rep(side==1, ifelse(side==1, 6, 3)),
	c(.01, .05, .1, .9, .95, .99), c(.01, .05, .1)),
	pal=ifelse(rep(side==1, ifelse(side==1, 1, length(p.cutoffs)+1)),
	"RdBu", rev(brewer.pal(length(p.cutoffs)+1,"Reds"))),
	test="Stouffer", branch.label=FALSE, tip.color=TRUE, edge.color=TRUE,
	tip.label.size=1, branch.label.size=1,  type="fan",
	use.edge.length=TRUE, edge.width=1, branch="edge", 
	root.edge=ifelse(type=="fan",FALSE,TRUE),
	branch.label.frame="none")

Arguments

tree	a phylogenetic tree of class phylo.
unsorted.pvalues	a data frame (or matrix) with tip labels in column 1 and p-values in column 2. The tip labels must correspond to the tip labels in tree.
adjust	a logical argument that controls whether there is p-value adjustment performed (TRUE) or not (FALSE).
side	a numerical argument that takes values 1 and 2, depending on whether the p-values in unsorted.pvalues are 1-sided or 2-sided, respectively. Only used in p-value adjustment if adjust = TRUE.
method	one of the p-value adjustment methods (used for multiple-hypothesis testing) found in p.adjust.methods ("holm", "hochberg", "hommel", "BH", "bonferroni", "BY", "fdr", and "none"). See help for p.adjust for more details on these methods. method is only used if adjust = TRUE.
p.cutoffs	a vector of increasing p-value cutoffs (excluding 0 and 1) to determine the ranges of p-values used in the coloring of the branches.
pal	one of the palettes from the RColorBrewer package (see brewer.pal.info for a list) or a vector of hexadecimal colors (or other valid R colors). These are the colors that are used to color the branches. The first color corresponds to the first range in p.cutoffs and so on.
test	a character string taking on "Hartung", "Stouffer", or "Fisher". This is the p-value combination method that will be used. In most cases, "Stouffer" will be most appropriate, unless adonis.tree indicates significant evidence of dependence among p-values, in which case "Hartung" is preferred.
branch.label	a logical argument that controls whether the branches are labeled (TRUE) or not (FALSE). This results in either edges or nodes being labeled, depending on the branch argument. The edge and node labeling is internal to class phylo, and are not necessarily sequential numbers. When branch="edge" is used, the tip edges are not labeled (to avoid clutter). Branch labels match those returned by export.inherit.
tip.color	a logical argument that controls whether the tips are colored (TRUE) or not (FALSE).
edge.color	a logical argument that controls whether the edges are colored (TRUE) or not (FALSE).
tip.label.size	a numerical argument that controls the (cex) size of the text of the tip labels.
branch.label.size	a numerical argument that controls the (cex) size of the text of the branch labels (see branch.label argument).
type	a character string that controls which type of plot will be produced. Possible values are "phylogram", "cladogram", "fan", "unrooted", and "radial". See plot.phylo.
use.edge.length	a logical argument that uses the original edge lengths from tree (TRUE) or not (FALSE). This has no effect if tree does not have edge lengths defined to begin with. Can be affected by root.edge, depending on type (see root.edge below).
edge.width	a numeric vector controlling width of plotted edges. This is passed to (plot.phylo).
branch	a character controlling branch definition: "edge" and "node" are the only options. This does not affect statistical methods, only the colors used in edge coloring. Prior to package version 1.2, only branch="node" was implemented.
root.edge	a logical argument that controls whether the root edge is plotted (TRUE) or not (FALSE). Note that root.edge=TRUE forces use.edge.length=FALSE when type is "phylogram", "cladogram", "fan", or "unrooted".
branch.label.frame	a character controlling the frame around the branch labels (only used when branch.label=TRUE). Only options "none", "circ", and "rect" are supported.

Details

The tip labels of tree (accessed via tree$tip.label) must have the same names (and the same length) as the tip labels in unsorted.pvalues, but may be in a different order. The p-values in column 2 of unsorted.pvalues obviously must be in the [0, 1] range. p.cutoffs takes values in the (0, 1) range. The default value for p.cutoffs is c(0.01, 0.05, 0.1, 0.9, 0.95, 0.99) if side is 1 and c(0.01, 0.05, 0.1) if side is 2. Thus, the ranges (when side is 1) are: [0, .01], (.01, .05], ..., (.99, 1]. These ranges correspond to the colors specified in pal. P-values in the [0, .01] range correspond to the left-most color if pal is a palette (view this via display.brewer.pal(x, pal) - where x is the number of colors to be used) or the first value in the vector if pal is a vector of colors. If pal is a vector of colors, then the length of pal should be one greater than the length of p.cutoffs. In other words, its length must be the same as the number of p-value ranges. An example of a color in hexadecimal format is "#B2182B". The default value of pal is "RdBu" (a divergent palette of reds and blues, with reds corresponding to small p-values) if side is 1 and the reverse of "Reds" (a sequential palette) if side is 2. The sequential palettes in RColorBrewer go from light to dark, so "Reds" is reversed so that the dark red corresponds to small p-values. It probably makes more sense to use a divergent palette when using 1-sided p-values and a sequential palette (reversed) when using 2-sided p-values. To create a vector of reversed colors from a palette with x number of colors and "PaletteName" as the name of the palette, use rev(brewer.pal(x, "PaletteName")). use.edge.length may be useful to get a more uniformly-shaped tree. plotSigTree assumes that each internal node has exactly two descendants. It also assumes that each internal node has a lower number than each of its ancestors (excluding tips).

The branch argument controls whether edge coloring corresponds to the combined p-value of the tips below the edge ("edge") or of the tips below the edge's leading (away from the tips) node ("node"). Note that if branch="node" is used, then both edges leaving a node will necessarily be colored the same.

To access the tutorial document for this package (including this function), type in R: vignette("SigTree")

Value

This function produces a phylogenetic tree plot.

Note

Extensive discussion of methods developed for this package are available in Jones (2012). In that reference, (and prior to package version number 1.1), this plotSigTree function was named plot.color; the name change was made to resolve S3 class issues.

For purposes of acknowledgments, it is worth noting here that the plotting done by plotSigTree relies internally on tools of the ape package (Paradis et al., 2004 Bioinformatics 20:289-290). To accomodate edge-specific coloring (as with the branch="edge" option), some of these ape package tools were adapted and re-named in the SigTree package. Specifically, see ?plotphylo2 and ?circularplot2.

Author(s)

John R. Stevens and Todd R. Jones

References

Stevens J.R., Jones T.R., Lefevre M., Ganesan B., and Weimer B.C. (2017) "SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree." Computational and Structural Biotechnology Journal 15:372-378.

Jones T.R. (2012) "SigTree: An Automated Meta-Analytic Approach to Find Significant Branches in a Phylogenetic Tree" (2012). MS Thesis, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/etd/1314

Examples

### To access the tutorial document for this package, type in R (not run here): 
# vignette('SigTree')

### Create tree, then data frame, then use plotSigTree to plot the tree
### Code for random tree and data frame
node.size <- 10
seed <- 109
# Create tree
set.seed(seed);
library(ape)
r.tree <- rtree(node.size)
# Create p-values data frame
set.seed(seed)
r.pval <- rbeta(node.size, .1, .1)
# Randomize the order of the tip labels
# (just to emphasize that labels need not be sorted)
set.seed(seed)
r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)

# Check for dependence among p-values; lack of significance here
# indicates default test="Stouffer" is appropriate; 
# otherwise, test="Hartung" would be more appropriate.
adonis.tree(r.tree,r.pvalues)

# Plot tree in default 'fan' type, with branches labeled
plotSigTree(r.tree, r.pvalues, edge.width=4, branch.label=TRUE)

# Plot tree in 'phylogram' type, with branch labels circled
plotSigTree(r.tree, r.pvalues, edge.width=4, branch.label=TRUE,
  type='phylo', branch.label.frame='circ')
  
# Plot tree in 'phylogram' type, with branch labels circled,
# and assuming original p-values were for 2-sided test
plotSigTree(r.tree, r.pvalues, edge.width=4, branch.label=TRUE,
  type='phylo', branch.label.frame='circ', side=2)

# Plot tree in 'phylogram' type, with branch labels boxed;
# also give custom significance thresholds, and use
# a Purple-Orange palette (dark purple for low p-vals
# to dark orange for high p-vals)
plotSigTree(r.tree, r.pvalues, edge.width=4, branch.label=TRUE,
  type='phylo', branch.label.frame='rect',
  p.cutoffs=c(.01,.025,.975,.99), pal='PuOr')
  

Example output

Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
[1] 0.4218578
Warning message:
system call failed: Cannot allocate memory 

SigTree documentation built on May 2, 2019, 5:40 a.m.