plot.wtd_lscp {Morphoscape}

Plot Adaptive Landscapes

Description

These plot plot methods plot an adaptive landscape, a weighted combination of functional surfaces. These landscape arise from calls to calc_lscp, calc_all_lscps, calcGrpWprime, and calcWprimeBy.

Usage

## S3 method for class 'wtd_lscp'
plot(x, alpha = 1, pt.col = "black", 
     interpolate = TRUE, contour = TRUE, ...)
## S3 method for class 'grp_Wprime'
plot(x, alpha = 1, pt.col = "black", 
     interpolate = TRUE, contour = TRUE, ...)
## S3 method for class 'by_Wprime'
plot(x, level, ncol = 1, alpha = 1,
     pt.col = "black", interpolate = TRUE, contour = TRUE, 
     ...)

Arguments

x

a wtd_lscp, grp_Wprime, or by_Wprime object, the output of a call to calc_lscp, calcGrpWprime, or calcWprimeBy, respectively.

alpha

the transparency of the points for the data sample. A number between 0 (fully transparent) and 1 (fully opaque). Passed to ggplot2::geom_point.

pt.col

the color of the points for the data sample. Passed to ggplot2::geom_point.

interpolate

whether to interpolate across pixels in the grid. Passed to ggplot2::geom_raster.

contour

whether to display contours in the grid.

level

which level of the by (subgrouping) variable to be plotted. If missing, all will be plotted.

ncol

when multiple subgroups are plotted, in how many columns should the plots be arranged.

...

ignored.

Details

These plotting functions are wrappers for ggplot2 raster plotting functions. For more precise control of raster plotting see ggplot2::geom_raster.

Value

A ggplot object that can be further adjusted using functions from ggplot2.

See Also

calc_lscp, calc_all_lscps, calcGrpWprime, and calcWprimeBy for the functions used to create the objects that are plotted

plot.kriged_surfaces for plotting functional surfaces prior to combining them into an adaptive landscape.

ggplot2::geom_raster, ggplot2::geom_point, and ggplot2::geom_contour for the underlying plotting functions.

Examples

data("warps")
data("turtles")

warps_fnc <- as_fnc_df(warps, func.names = c("hydro", "fea"))

kr_surf <- krige_surf(warps_fnc, new_data = turtles)

weights <- c(hydro = .5, fea = .5)

w_lscp <- calc_lscp(kr_surf, weights = weights)

plot(w_lscp)
plot(w_lscp, countour = FALSE, pt.col = "white")

# See help("calc_lscp"), help("calcGrpWprime"), and 
# help("calcWprimeBy") for examples when used with
# those functions