Plot diversity across sites.

Source: R/plotgg.r

Plot results of of permuting site diversity accross sites.

# S3 method for site.diversity
plotgg(sitediv, p = c(0.025, 0.975), alpha = 0.2,
  theme = theme_blackbox(), confints = TRUE)

Arguments

sitediv

A site.diversity object
p

Vector of length 2 indicating the confidence interval boundaries.
alpha

alpha paramater for transparency in ggplot2.
theme

theme to use for the plot.
confints

Logical indicating whether confidence intervals must be plotted.

Value

A ggplot2 plot object.

See also

site_diversity, compare_site_diversity

Examples

data(Rhizo)
data(Rhizo.map)
data(Rhizo.tax)
Dat <- create_dataset(Rhizo,Rhizo.map,Rhizo.tax)
sitediv.accession <- compare_site_diversity(Dat = Dat,factor = "accession", divfun = total_richness, 20)
plotgg(sitediv.accession)

divfun <- function(x){
  if(!is.null(ncol(x)))
    x <- rowSums(x)
  s <- vegan::diversity(x)
  return(s)
}
sitediv.accession <- compare_site_diversity(Dat = Dat,factor = "accession", divfun = divfun, 20)
plotgg(sitediv.accession, alpha = 0.3) +
  scale_color_brewer(palette = "Set3") +
  scale_fill_brewer(palette = "Set3")