EcotoneFinder (version 0.2.3)

plotSlope: Plotting component for Slope

Description

Plotting component for Slope

Usage

plotSlope(ecotoneslope, plot.data = FALSE, plot.method = c("none",
  "dca_slope", "fanny_slope", "vegclust_slope", "cmeans_slope",
  "diversity_slope"), axis.number = 1, magnification = 500,
  col.data = "black", col.method = c("red", "blue"), title = NULL,
  ylab = "Species", xlab = "Gradient", na.rm = FALSE, alone = TRUE,
  ...)

Arguments

ecotoneslope

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

plot.data

Logical. Should the data be plotted.

plot.method

Analysis method to be plotted from the Slope results. Must be one or several of "none", "dca_slope","fanny_slope","vegclust_slope", "cmeans_slope" or "diversity_slope".

axis.number

Number of axis to plot from the DCA.

magnification

Magnification coefficient for the method. Usefull if the data are being plotted.

col.data

Colors to be used for the data. See CommunityColor function.

col.method

Colors to be used for the methods.

title

An overall title for the plot. See plot.

ylab

A title for the y-axis. See plot.

xlab

A title for the x-axis. See plot.

na.rm

Logical. Should NAs be removed.

alone

Logical. If FALSE, lines are added to an existing plot.

...

Additional argument to be passed to the plot function.

Value

A plot with the Slope results along the gradient, and optionally, the data.

Details

Internal component of the PlotEcotone function for the plotting of the Slope analyses. Use PlotEcotone directly for more options.

Examples

# NOT RUN {
 ######## Artificial dataset & analysis:
 SyntheticTrial <- SyntheticData(SpeciesNum = 20, CommunityNum = 3,
                                 SpCo = NULL, Length = 500,
                                 Parameters = list(a=rep(60, 3),
                                                   b=c(0,250,500),
                                                   c=rep(0.03,3)),
                                 dev.c = .015, pal = c("#008585", "#FBF2C4", "#C7522B"))

 SyntheticEcoFinder <- EcotoneFinder(SyntheticTrial[,-1],
                                     dist = SyntheticTrial$Distance,
                                     method = "all", groups = 3,
                                     standardize = "hellinger",
                                     diversity = "all")

 ### Derivatives:
 SyntheticSlope <- Slope(SyntheticEcoFinder, method = "all",
                         axis.number = 2, diversity = "all")

### Plot:
require(colorspace)
plotSlope(SyntheticSlope, plot.data = FALSE,
          plot.method = c("cmeans_slope", "vegclust_slope"),
          col.method = terrain_hcl(3))


# }