ggplot2 formatting. Note that this
function is a performance and interface revision to
plot_network, which requires an
igraph object as its first
argument. This new function is more in-line with other
plot_* functions in the
phyloseq-package, in that its first/main
argument is a phyloseq-class instance.
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. However, network line thickness and
opacity is scaled according to the similarity of vertices
(either samples or taxa), helping to temper, somewhat,
the effect of the threshold. Also note that the choice of
network layout algorithm can have a large effect on the
impression and interpretability of the network graphic,
and you may want to familiarize yourself with some of
these options (see the laymeth argument).
plot_net(physeq, distance = "bray", type = "samples", maxdist = 0.7, laymeth = "fruchterman.reingold", color = NULL, shape = NULL, rescale = FALSE, point_size = 5, point_alpha = 1, point_label = NULL, hjust = 1.35, title = NULL)phyloseq-class object that you want to
represent as a network."bray". Can
be either a distance method supported by
distance, or an already-computed
dist-class with labels that match the
indices implied by both the physeq and type
arguments (that is, either sample or taxa names). If you
used distance to pre-calculate
your distance, and the same type
argument as provided here, then they will match.0.7. The
maximum distance value between two vertices to connect
with an edge in the graphic."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."fruchterman.reingold". A character string that
indicates the method that will determine the placement of
vertices, typically based on conectedness of vertices and
the number of vertices. This is an interesting topic, and
there are lots of options. See
igraph-package for related topics in
general, and see layout.auto for
descriptions of various alternative layout method options
supported here. The character string argument should
match exactly the layout function name with the
"layout." omitted. Try laymeth="list" to
see a list of options.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).FALSE.
Whether to rescale the distance values to be [0,
1], in which the min value is close to zero and the max
value is 1.4. The size
of the vertex points.1. A value
between 0 and 1 for the alpha transparency of the vertex
points.NULL. The
variable name in physeq covariate data to map to
vertex labels.1.35. The amount
of horizontal justification to use for each label.NULL. Character
string. The main title for the graphic.data(enterotype)
plot_net(enterotype, color="SeqTech", maxdist = 0.3)
plot_net(enterotype, color="SeqTech", maxdist = 0.3, laymeth = "auto")
plot_net(enterotype, color="SeqTech", maxdist = 0.3, laymeth = "svd")
plot_net(enterotype, color="SeqTech", maxdist = 0.3, laymeth = "circle")
plot_net(enterotype, color="SeqTech", shape="Enterotype", maxdist = 0.3, laymeth = "circle")
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