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.
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)igraph-class object
created either by the convenience wrapper
make_network, or directly by the tools in
the igraph-package.NULL. A
phyloseq-class object on which g is
based."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.NULL. The name of
the sample variable in physeq to use for color
mapping of points (graph vertices).NULL. The name of
the sample variable in physeq to use for shape
mapping. of points (graph vertices).4. The size
of the vertex points.1. A value
between 0 and 1 for the alpha transparency of the vertex
points."value". The name
of the sample variable in physeq to use for
labelling the vertex points.1.35. The amount
of horizontal justification to use for each label.0.3. The
line thickness to use to label graph edges.color. The
name of the sample variable in physeq to use for
color mapping of lines (graph edges).0.4. The
transparency level for graph-edge lines.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:NULL. Character
string. The main title for the graphic.ggplot2 plot representing the network,
with optional mapping of variable(s) to point color or
shape.
The code most directly used/modified was first posted here: http://www.r-bloggers.com/basic-ggplot2-network-graphs/
make_network
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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