plot_taxa_ridges {TITAN2} | R Documentation |
Taxon change point ridge plots
Description
Taxon change point ridge plots
Usage
plot_taxa_ridges(
titan.out,
z1 = TRUE,
z2 = TRUE,
z1_fill_low = "lightblue",
z1_fill_high = "black",
z2_fill_low = "pink",
z2_fill_high = "red",
xlabel = "Environmental Gradient",
n_ytaxa = 90,
printspp = FALSE,
grid = TRUE,
d_lines = FALSE,
trans = "identity",
xaxis = !grid,
xlim,
breaks = ggplot2::waiver(),
bw,
rel_heights,
...,
axis.text.x,
axis.text.y,
axis.title.x,
axis.title.y
)
Arguments
titan.out |
A TITAN output object. |
z1 |
A logical specifying whether decreasing taxa should be plotted. |
z2 |
A logical specifying whether increasing taxa should be plotted. |
z1_fill_low , z1_fill_high , z2_fill_low , z2_fill_high |
Respective fill
colors passed to |
xlabel |
A character string for the x axis label. |
n_ytaxa |
The maximum number of taxa to be plotted. |
printspp |
A logical specifying whether the sppmax table should be printed. |
grid |
The |
d_lines |
Argument to pass to |
trans |
a scale transformation to be applied to the x-axis through
ggplot2. e.g. |
xaxis |
Logical; should the x-axis be plotted? |
xlim |
x axis limits, e.g. |
breaks |
Argument to pass to |
bw |
The bandwidth of used in the kernel density estimate; see
|
rel_heights |
Argument to pass to |
... |
Arguments to pass to |
axis.text.x , axis.text.y , axis.title.x , axis.title.y |
Font sizes of respective axis text. Passed as the size argument to the ggplot2 thematic elements of the same name. Defaults to current default ggplot2 theme. |
Value
A plot of decreasing and/or increasing taxon-specific change points along the environmental gradient.
Note
Should not be used with output objects from TITAN v1.0.
Author(s)
M. Baker, R. King, D. Kahle
References
Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37.
King, RS and ME Baker 2010. Considerations for identifying and interpreting ecological community thresholds. Journal of the North American Benthological Association 29(3):998-1008.
See Also
Examples
data(glades.titan)
# basic usage
plot_taxa_ridges(glades.titan)
## Not run: reduce R CMD check time
# manipulating the x axis thematic components
plot_taxa_ridges(glades.titan, grid = FALSE)
plot_taxa_ridges(glades.titan, xaxis = TRUE)
# applying scale transformations
plot_taxa_ridges(glades.titan, trans = "log10", xlim = c(1,150))
# removing z2
plot_taxa_ridges(glades.titan, z2 = FALSE, trans = "sqrt", xlim = c(0, 150))
# more styling
plot_taxa_ridges(glades.titan,
axis.text.x = 12,
axis.text.y = 4,
axis.title.x = 14,
xlabel = expression(paste("Surface water total phosphorus ("*mu*"g/l)"))
)
## End(Not run)