plot_tree | R Documentation |
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.
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")
physeq |
(Required). The data about which you want to
plot and annotate a phylogenetic tree, in the form of a
single instance of the |
method |
(Optional). Character string. Default |
nodelabf |
(Optional). A function. Default |
color |
(Optional). Character string. Default |
shape |
(Optional). Character string. Default |
size |
(Optional). Character string. Default |
min.abundance |
(Optional). Numeric.
The minimum number of individuals required to label a point
with the precise number.
Default is |
label.tips |
(Optional). Character string. Default is |
text.size |
(Optional). Numeric. Should be positive. The
size parameter used to control the text size of taxa labels.
Default is |
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 |
ladderize |
(Optional). Boolean or character string (either
|
plot.margin |
(Optional). Numeric. Default is |
title |
(Optional). Default |
treetheme |
(Optional).
A custom |
justify |
(Optional). A character string indicating the
type of justification to use on dodged points and tip labels.
A value of |
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
.
A ggplot
2 plot.
plot.phylo
There are many useful examples of phyloseq tree graphics in the phyloseq online tutorials.
# # Using plot_tree() with the esophagus dataset. # # Please note that many more interesting examples are shown # # in the online tutorials" # # 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.