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")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)."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.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.NULL. The name of the variable in physeq to
map to point color. Supported options here also include
the reserved special variables of psmelt.NULL. The name of the variable in physeq to
map to point shape. Supported options here also include
the reserved special variables of psmelt.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.Inf, meaning that no
points will have their abundance labeled. If a vector,
only the first element is used.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.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.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.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 FALSE, no
ladderization is applied. When set to "left", the
reverse direction (``left'' ladderization) is applied.
This argument is passed on to tree_layout.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.NULL. Character
string. The main title for the graphic."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.ggplot2 plot.
plot_tree has since been re-written. For
details see tree_layout.
plot.phyloThere 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)
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