View source: R/plot_taxa_ridges.R
plot_taxa_ridges | R Documentation |
Taxon change point ridge plots
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
)
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. |
A plot of decreasing and/or increasing taxon-specific change points along the environmental gradient.
Should not be used with output objects from TITAN v1.0.
M. Baker, R. King, D. Kahle
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.
plot_sumz()
, plot_cps()
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)
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