plot.cgr: Plot graph of direct species associations.

In ecoCopula: Graphical Modelling and Ordination using Copulas

Plot graph of direct species associations.

Description

Plot graph of direct species associations.

Usage

## S3 method for class 'cgr'
plot(
  x,
  P = NULL,
  vary.edge.lwd = FALSE,
  edge.col = c("light blue", "pink"),
  label = colnames(x$obj$fitted),
  vertex.col = "blue",
  label.cex = 0.8,
  edge.lwd = ifelse(vary.edge.lwd, 10, 4),
  edge.lty = c(1, 1),
  ...
)

Arguments

x	is a cgr object, e.g. from output of cgr.
P	locations of graph nodes, if NULL (default) these are generated with a Fruchterman Reingold algorithm.
vary.edge.lwd	is logical, TRUE will vary line width according to the strength of partial correlation, default (FALSE) uses fixed line width.
edge.col	takes two colours as arguments - the first is the colour used for positive partial correlations, the second is the colour of negative partial correlations.
label	is a vector of labels to apply to each variable, defaulting to the column names supplied in the data.
vertex.col	the colour of graph nodes.
label.cex	is the size of labels.
edge.lwd	is line width, defaulting to 10*partial correlation when varying edge width, and 4 otherwise.
edge.lty	is a vector of two integers specifying the line types for positive and negative partial correlations, respectively. Both default to solid lines.
...	other parameters to be passed through to plotting gplot, in particular pad, the amount to pad the plotting range is useful if labels are being clipped. For details see the gplot help file.

Value

a plot of species associations after accounting for the effect of all other species, positive/negative are blue/pink. The matrix of node positions (P) is returned silently.

See Also

gplot, cgr

Examples

abund <- spider$abund[,1:5]
spider_mod <- stackedsdm(abund,~1, data = spider$x, ncores=2) 
spid_graph=cgr(spider_mod)
plot(spid_graph, edge.col=c("forestgreen","darkorchid4"), 
                 vertex.col = "black",vary.edge.lwd=TRUE)
                 

library(tidyr)
library(tidygraph)
library(ggraph)

igraph_out<-spid_graph$best_graph$igraph_out

igraph_out %>% ggraph('fr') + # see ?layout_tbl_graph_igraph
   geom_edge_fan0(aes( colour = partcor, width=partcor)) +
   scale_edge_width(range = c(0.5, 3))+
   scale_edge_color_gradient2(low="#b2182b",mid="white",high="#2166ac")+
   geom_node_text(aes(label=name), repel = TRUE)+
   geom_node_point(aes(size=1.3))+
   theme_void() +
   theme(legend.position = 'none')

ecoCopula documentation built on March 18, 2022, 6:56 p.m.