ggiNEXT: Alpha diversity ggplot2 extension for an iNEXT object this...

In rusher321/microbiotaPair: An R Package for Simplified Microbiome Analysis Workflows on Intervention Study

Alpha diversity ggplot2 extension for an iNEXT object this function focked from the iNEXT package ggiNEXT: the ggplot extension for iNEXT Object to plot sample-size- and coverage-based rarefaction/extrapolation curves along with a bridging sample completeness curve

Description

Alpha diversity ggplot2 extension for an iNEXT object this function focked from the iNEXT package ggiNEXT: the ggplot extension for iNEXT Object to plot sample-size- and coverage-based rarefaction/extrapolation curves along with a bridging sample completeness curve

Usage

ggiNEXT(
  x,
  type = 1,
  se = TRUE,
  facet.var = "none",
  color.var = "site",
  grey = FALSE,
  usercolor = NULL
)

Arguments

x	an iNEXT object computed by iNEXT.
type	three types of plots: sample-size-based rarefaction/extrapolation curve (type = 1); sample completeness curve (type = 2); coverage-based rarefaction/extrapolation curve (type = 3).
se	a logical variable to display confidence interval around the estimated sampling curve.
facet.var	create a separate plot for each value of a specified variable: no separation (facet.var="none"); a separate plot for each diversity order (facet.var="order"); a separate plot for each site (facet.var="site"); a separate plot for each combination of order x site (facet.var="both").
color.var	create curves in different colors for values of a specified variable: all curves are in the same color (color.var="none"); use different colors for diversity orders (color.var="order"); use different colors for sites (color.var="site"); use different colors for combinations of order x site (color.var="both").
grey	a logical variable to display grey and white ggplot2 theme.
usercolor	a vector including the color that user define
...	other arguments passed on to methods. Not currently used.

Value

a ggplot2 object

Examples

library(iNEXT)
data(spider)
# single-assemblage abundance data
out1 <- iNEXT(spider$Girdled, q = 0, datatype = "abundance")
ggiNEXT(x = out1, type = 1)
ggiNEXT(x = out1, type = 2)
ggiNEXT(x = out1, type = 3)

## Not run: 
# single-assemblage incidence data with three orders q
data(ant)
size <- round(seq(10, 500, length.out = 20))
y <- iNEXT(ant$h500m, q = c(0, 1, 2), datatype = "incidence_freq", size = size, 
    se = FALSE)
ggiNEXT(y, se = FALSE, color.var = "order")

# multiple-assemblage abundance data with three orders q
z <- iNEXT(spider, q = c(0, 1, 2), datatype = "abundance")
myggiNEXT.iNEXT(z, facet.var = "site", color.var = "order")

## End(Not run)

rusher321/microbiotaPair documentation built on July 24, 2024, 8:40 p.m.