plot_tree: Plot a phylogenetic tree with optional annotations

In mikemc/speedyseq: Faster implementations of phyloseq functions

Plot a phylogenetic tree with optional annotations

Description

There are many useful examples of phyloseq tree graphics in the phyloseq online tutorials. This function is intended to facilitate easy graphical investigation of the phylogenetic tree, as well as sample data. Note that for phylogenetic sequencing of samples with large richness, some of the options in this function will be prohibitively slow to render, or too dense to be interpretable. A rough “rule of thumb” is to use subsets of data with not many more than 200 OTUs per plot, sometimes less depending on the complexity of the additional annotations being mapped to the tree. It is usually possible to create an unreadable, uninterpretable tree with modern datasets. However, the goal should be toward parameter settings and data subsets that convey (honestly, accurately) some biologically relevant feature of the data. One of the goals of the phyloseq-package is to make the determination of these features/settings as easy as possible.

Usage

plot_tree(
  physeq,
  method = "sampledodge",
  nodelabf = NULL,
  color = NULL,
  shape = NULL,
  size = NULL,
  min.abundance = Inf,
  label.tips = NULL,
  text.size = NULL,
  sizebase = 5,
  base.spacing = 0.02,
  ladderize = FALSE,
  plot.margin = 0.2,
  title = NULL,
  treetheme = NULL,
  justify = "jagged"
)

Arguments

physeq	(Required). The data about which you want to plot and annotate a phylogenetic tree, in the form of a single instance of the phyloseq-class, containing at minimum a phylogenetic tree component (try phy_tree). One of the major advantages of this function over basic tree-plotting utilities in the ape-package is the ability to easily annotate the tree with sample variables and taxonomic information. For these uses, the physeq argument should also have a sample_data and/or tax_table component(s).
method	(Optional). Character string. Default "sampledodge". The name of the annotation method to use. This will be expanded in future versions. Currently only "sampledodge" and "treeonly" are supported. The "sampledodge" option results in points drawn next to leaves if individuals from that taxa were observed, and a separate point is drawn for each sample.
nodelabf	(Optional). A function. Default NULL. If NULL, the default, a function will be selected for you based upon whether or not there are node labels in phy_tree(physeq). For convenience, the phyloseq package includes two generator functions for adding arbitrary node labels (can be any character string), nodeplotdefault; as well as for adding bootstrap values in a certain range, nodeplotboot. To not have any node labels in the graphic, set this argument to nodeplotblank.
color	(Optional). Character string. Default NULL. The name of the variable in physeq to map to point color. Supported options here also include the reserved special variables of psmelt.
shape	(Optional). Character string. Default NULL. The name of the variable in physeq to map to point shape. Supported options here also include the reserved special variables of psmelt.
size	(Optional). Character string. Default NULL. The name of the variable in physeq to map to point size. A special argument "abundance" is reserved here and scales point size using abundance in each sample on a log scale. Supported options here also include the reserved special variables of psmelt.
min.abundance	(Optional). Numeric. The minimum number of individuals required to label a point with the precise number. Default is Inf, meaning that no points will have their abundance labeled. If a vector, only the first element is used.
label.tips	(Optional). Character string. Default is NULL, indicating that no tip labels will be printed. If "taxa_names", then the name of the taxa will be added to the tree; either next to the leaves, or next to the set of points that label the leaves. Alternatively, if this is one of the rank names (from rank_names(physeq)), then the identity (if any) for that particular taxonomic rank is printed instead.
text.size	(Optional). Numeric. Should be positive. The size parameter used to control the text size of taxa labels. Default is NULL. If left NULL, this function will automatically calculate a (hopefully) optimal text size given the vertical constraints posed by the tree itself. This argument is included in case the automatically-calculated size is wrong, and you want to change it. Note that this parameter is only meaningful if label.tips is not NULL.
sizebase	(Optional). Numeric. Should be positive. The base of the logarithm used to scale point sizes to graphically represent abundance of species in a given sample. Default is 5.
base.spacing	(Optional). Numeric. Default is 0.02. Should be positive. This defines the base-spacing between points at each tip/leaf in the the tree. The larger this value, the larger the spacing between points. This is useful if you have problems with overlapping large points and/or text indicating abundance, for example. Similarly, if you don't have this problem and want tighter point-spacing, you can shrink this value.
ladderize	(Optional). Boolean or character string (either FALSE, TRUE, or "left"). Default is FALSE. This parameter specifies whether or not to ladderize the tree (i.e., reorder nodes according to the depth of their enclosed subtrees) prior to plotting. This tends to make trees more aesthetically pleasing and legible in a graphical display. When TRUE or "right", ⁠right'' ladderization is used. When set to \code{FALSE}, no ladderization is applied. When set to \code{"left"}, the reverse direction (⁠left” ladderization) is applied. This argument is passed on to tree_layout.
plot.margin	(Optional). Numeric. Default is 0.2. Should be positive. This defines how much right-hand padding to add to the tree plot, which can be required to not truncate tip labels. The margin value is specified as a fraction of the overall tree width which is added to the right side of the plot area. So a value of 0.2 adds twenty percent extra space to the right-hand side of the plot.
title	(Optional). Default NULL. Character string. The main title for the graphic.
treetheme	(Optional). A custom ggplot2 theme layer to use for the tree. Supplants any default theme layers used within the function. A value of NULL uses a default, minimal-annotations theme. If anything other than a them or NULL, the current global ggplot2 theme will result.
justify	(Optional). A character string indicating the type of justification to use on dodged points and tip labels. A value of "jagged", the default, results in these tip-mapped elements being spaced as close to the tips as possible without gaps. Currently, any other value for justify results in a left-justified arrangement of both labels and points.

Details

This function received an early development contribution from the work of Gregory Jordan via the ggphylo package. plot_tree has since been re-written. For details see tree_layout.

Value

A ggplot2 plot.

See Also

plot.phylo

There are many useful examples of phyloseq tree graphics in the phyloseq online tutorials.

Examples

# Using plot_tree() with the esophagus dataset.
# Please note that many more interesting examples are shown in the online
# tutorials at http://joey711.github.io/phyloseq/plot_tree-examples
data(esophagus)
# plot_tree(esophagus)
# plot_tree(esophagus, color="Sample")
# plot_tree(esophagus, size="Abundance")
# plot_tree(esophagus, size="Abundance", color="samples")
plot_tree(esophagus, size="Abundance", color="Sample", base.spacing=0.03)
plot_tree(esophagus, size="abundance", color="samples", base.spacing=0.03)

mikemc/speedyseq documentation built on April 22, 2024, 6:40 p.m.