plotgg.site.diversity: Plot diversity across sites.

In surh/AMOR: Abundance Matrix Operations in R

Plot diversity across sites.

Description

Plot results of of permuting site diversity accross sites.

Usage

## S3 method for class '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.

Author(s)

Sur from Dangl Lab.

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")

surh/AMOR documentation built on Feb. 21, 2023, 6:31 a.m.