Description Usage Arguments Value References See Also Examples
There are many useful examples of phyloseq network graphics in the
phyloseq online tutorials.
A custom plotting function for displaying networks
using advanced ggplot
2 formatting.
The network itself should be represented using
the igraph
package.
For the phyloseq-package
it is suggested that the network object
(argument g
)
be created using the
make_network
function,
and based upon sample-wise or taxa-wise microbiome ecological distances
calculated from a phylogenetic sequencing experiment
(phyloseq-class
).
In this case, edges in the network are created if the distance between
nodes is below a potentially arbitrary threshold,
and special care should be given to considering the choice of this threshold.
1 2 3 4 5 |
g |
(Required). An |
physeq |
(Optional). Default |
type |
(Optional). Default |
color |
(Optional). Default |
shape |
(Optional). Default |
point_size |
(Optional). Default |
alpha |
(Optional). Default |
label |
(Optional). Default |
hjust |
(Optional). Default |
line_weight |
(Optional). Default |
line_color |
(Optional). Default |
line_alpha |
(Optional). Default |
layout.method |
(Optional). Default |
title |
(Optional). Default
|
A ggplot
2 plot representing the network,
with optional mapping of variable(s) to point color or shape.
This code was adapted from a repo original hosted on GitHub by Scott Chamberlain: https://github.com/SChamberlain/gggraph
The code most directly used/modified was first posted here: http://www.r-bloggers.com/basic-ggplot2-network-graphs/
1 2 3 4 5 6 | data(enterotype)
ig <- make_network(enterotype, max.dist=0.3)
plot_network(ig, enterotype, color="SeqTech", shape="Enterotype", line_weight=0.3, label=NULL)
# Change distance parameter
ig <- make_network(enterotype, max.dist=0.2)
plot_network(ig, enterotype, color="SeqTech", shape="Enterotype", line_weight=0.3, label=NULL)
|
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