plot_network {phyloseq} | R Documentation

## 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 `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.

### 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 `ggplot`2 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/

### See Also

`make_network`

### 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)

[Package phyloseq version 1.26.1 Index]