phyloseq: plot_network – R documentation

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plot_network

Microbiome Network Plot using ggplot2

Description

There are many useful examples of phyloseq network graphics in the phyloseq online tutorials. A custom plotting function for displaying networks using advanced ggplot2 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.

Usage

plot_network(g, physeq=NULL, type="samples", 
	color=NULL, shape=NULL, point_size=4, alpha=1,
	label="value", hjust = 1.35, 
	line_weight=0.5, line_color=color, line_alpha=0.4,
	layout.method=layout.fruchterman.reingold, title=NULL)

Arguments

`g`	(Required). An `igraph`-class object created either by the convenience wrapper `make_network`, or directly by the tools in the igraph-package.
`physeq`	(Optional). Default `NULL`. A `phyloseq-class` object on which `g` is based.
`type`	(Optional). Default `"samples"`. Whether the network represented in the primary argument, `g`, is samples or taxa/OTUs. Supported arguments are `"samples"`, `"taxa"`, where `"taxa"` indicates using the taxa indices, whether they actually represent species or some other taxonomic rank.
`color`	(Optional). Default `NULL`. The name of the sample variable in `physeq` to use for color mapping of points (graph vertices).
`shape`	(Optional). Default `NULL`. The name of the sample variable in `physeq` to use for shape mapping. of points (graph vertices).
`point_size`	(Optional). Default `4`. The size of the vertex points.
`alpha`	(Optional). Default `1`. A value between 0 and 1 for the alpha transparency of the vertex points.
`label`	(Optional). Default `"value"`. The name of the sample variable in `physeq` to use for labelling the vertex points.
`hjust`	(Optional). Default `1.35`. The amount of horizontal justification to use for each label.
`line_weight`	(Optional). Default `0.3`. The line thickness to use to label graph edges.
`line_color`	(Optional). Default `color`. The name of the sample variable in `physeq` to use for color mapping of lines (graph edges).
`line_alpha`	(Optional). Default `0.4`. The transparency level for graph-edge lines.
`layout.method`	(Optional). Default `layout.fruchterman.reingold`. A function (closure) that determines the placement of the vertices for drawing a graph. Should be able to take an `igraph`-class as sole argument, and return a two-column coordinate matrix with `nrow` equal to the number of vertices. For possible options already included in `igraph`-package, see the others also described in the help file:
`title`	(Optional). Default `NULL`. Character string. The main title for the graphic. `layout.fruchterman.reingold`

Value

A ggplot2 plot representing the network, with optional mapping of variable(s) to point color or shape.

References

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/

Examples

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)

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23