EcotoneFinder (version 0.2.3)

ggEcotone: GGplot method for EcotoneFinder

Description

GGplot method for EcotoneFinder

Usage

ggEcotone(ecotonefinder, slope = NULL, plot.data = FALSE,
  method = c("none", "dca", "fanny", "vegclust", "cmeans", "diversity",
  "dca_slope", "fanny_slope", "vegclust_slope", "cmeans_slope",
  "diversity_slope"), axis.number = 1, diversity = c("Shannon",
  "SpeciesRichness", "ExpShannon", "Pielou", "SpeciesRichness_slope",
  "Shannon_slope", "ExpShannon_slope", "Pielou_slope"), facet = NULL,
  col = "black", title = NULL, xlab = NULL, ylab = NULL,
  return.plot = TRUE)

Arguments

ecotonefinder

list containing elements named in the same way than the EcotoneFinder function outcomes.

slope

list containing elements named in the same way than the Slope function outcomes.

plot.data

Logical. Should the data be plotted? Default to FALSE.

method

Analysis method to be plotted from the EcotoneFinder results or the Slope results. Must be one or several of "none","dca","fanny","vegclust", "cmeans","diversity", "dca_slope","fanny_slope","vegclust_slope", "cmeans_slope" or "diversity_slope".

axis.number

Number of DCA axis to be plotted. Must be between 1 and 4. Default to 1.

diversity

diversity indice to be plotted, if the method argument contains "diversity" or "diversity_slope". Must be one or several of "Shannon", "SpeciesRichness", "ExpShannon", "Pielou", "all"

facet

Character vector of method names indicating how the plot should be facetted. Can be provided as a list if several methods are to be plotted on the same facets. Can contain "data" if plot.data = T. If NULL, no facets are returned. See details.

col

Color palette to be used for plotting. Must be either of length 1, of the same lenght than the number of facets (when provided), or of the same length than the number of species (if plot.data = TRUE), or than the number of groups or axis plotted with the method argument. See details.

title

Main title for the plot

xlab

A title for the x-axis. See plot.

ylab

A title for the y-axis. See plot.

return.plot

Logical. If TRUE, the plot is directly plotted. If FALSE, the plot is stored as a ggplot object. Default to FALSE. See details.

Value

A ggplot object.

Details

The ggEcotone function is intended to facilitate the plotting of EcotoneFinder lists with the use of the ggplot2 grammar. It either directly print its outputs (if plot = TRUE), or returns a ggplot object that can be further modified (if plot = FALSE). The latter allows for the addition of other ggplot2 layers to personalise graphical outputs (see examples).

Facetting options are implemented to allow for the separation of the different method outputs and facilitate comparisons. The facet parameter accepts lists, with each element of the list corresponding to a facet and consisting of the names of the methods to be plotted on that facet.

The col parameter allows for basic control over the colors of the lines. ggplot internally recycles colour vectors for each new facets, making it difficult to precisely control colours in facetted plots. Plotting the outputs on several graphs and arranging them on a grid is the best way to produce "facetted" plots with different coulour schemes. See examples.

Examples

# NOT RUN {
#### Artificial dataset:
 SyntheticTrial <- SyntheticData(SpeciesNum = 21, CommunityNum = 3,
                                 SpCo = NULL ,Length = 500,
                                 Parameters = list(a=rep(60, 3),
                                                   b=c(0,250,500),
                                                   c=rep(0.015,3)),
                                 pal = c("#008585", "#FBF2C4", "#C7522B"))

 ## Analyses:
 EcoFinder <- EcotoneFinder(data = SyntheticTrial[,-1],
                            dist = SyntheticTrial$Distance,
                            method = "all", groups = 3,
                            standardize = "hellinger", diversity = "all")

 ## Slope calculation:
 EcoSlope <- Slope(EcoFinder, method = "all", axis.number = 2,
                   diversity = "all")

 ## Plots:
 
# }
# NOT RUN {
 require(ggplot2)
 require(colorspace)
 # Species Distributions and Fuzzy clusters:
 Plot <- ggEcotone(EcoFinder, slope = EcoSlope, plot.data = TRUE,
                   method = c("cmeans", "fanny"),
                   col = c("#D33F6A", "#E99A2C", "#E2E6BD"),
                   facet = list(c("data"), c("cmeans", "fanny")),
                   title = "Species distribution and fuzzy clusters",
                   xlab = "Gradient", ylab = "Membership grades") +
   theme(plot.title = element_text(hjust = 0.5, face="bold")) +
   theme_bw()
 Plot

 # Fuzzy clusters & derivatives:
 Plot <- ggEcotone(EcoFinder, slope = EcoSlope, plot.data = FALSE,
                   method = c("cmeans", "cmeans_slope"),
                   col = c("#D33F6A", "#E99A2C", "#E2E6BD"),
                   facet = c("cmeans", "cmeans_slope"),
                   title = "fuzzy clusters and derivatives",
                   xlab = "Gradient", ylab = "Membership grades") +
   theme(plot.title = element_text(hjust = 0.5, face="bold")) +
   theme_bw()
 Plot

 # Multiplot layout:
 GG1 <- ggEcotone(EcoFinder, slope = EcoSlope, plot.data = TRUE,
                  method = c("none"), col = heat_hcl(21), facet = NULL,
                  title = "Species distributions", xlab = NULL,
                  ylab = "Abundances") +
   theme(plot.title = element_text(hjust = 0.5, face="bold")) +
   theme_bw()

 GG2 <- ggEcotone(EcoFinder, slope = EcoSlope, plot.data = FALSE,
                  method = c("cmeans"), col = c("#023FA5", "#BEC1D4", "#D6BCC0"),
                  facet = NULL, title = "Fuzzy clusters", xlab = NULL,
                  ylab = "Membership grades") +
   theme(plot.title = element_text(hjust = 0.5, face="bold")) +
   theme_bw()

 GG3 <- ggEcotone(EcoFinder, slope = EcoSlope, plot.data = FALSE,
                  method = c("diversity"),
                  col = c("#26A63A", "#B4B61A"), facet = NULL,
                  diversity=c("SpeciesRichness", "ExpShannon"),
                  title = "diversity indices", xlab = "Gradient",
                  ylab = "Index scores") +
   theme(plot.title = element_text(hjust = 0.5, face="bold")) +
   theme_bw()

 require(Rmisc)
 Rmisc::multiplot(GG1,GG2,GG3)
 
# }
# NOT RUN {
# }