mgcViz (version 0.2.0)

plotSlice: Plotting sequence of slices of 2D smooth effect

Description

This function allows to slice a multi-dimensional (D > 2) smooth effect, and to plot the resulting sequence of 2D slices in an array of plots.

Usage

plotSlice(x, fix, a.facet = list(), ...)

Value

An objects of class plotSmooth.

Arguments

x

a smooth effect object, extracted using sm.

fix

a named list of vectors, where the i-th entry of each vector indicates the value we want to use for the covariate for i-th slice. When plotting a smooth in (d+2) dimensions, we need d vectors, because d variables must be fixed. All vectors must have either the same length (the number of slices) or length 1. fix can contain at most 2 vectors, so if d>=5, we need to set at least one covariate to a scalar.

a.facet

arguments to be passed to ggplot2::facet_wrap or ggplot2::facet_grid. The former gets called when fix contains one vector, the latter when fix contains two vectors.

...

further arguments to be passed to plot.mgcv.smooth.MD.

Examples

if (FALSE) {
### Example 1: plotting slices of 3D smooth
# Simulate data and fit GAM
library(mgcViz)
n <- 1e3
x <- rnorm(n); y <- rnorm(n); z <- rnorm(n)
ob <- (x-z)^2 + (y-z)^2 + rnorm(n)
b <- gam(ob ~ s(x, y, z))
v <- getViz(b)

# Get plot of slices and add layers
pl <- plotSlice(x = sm(v, 1), 
                fix = list("z" = seq(-2, 2, length.out = 9)))
pl + l_fitRaster() + l_fitContour() + l_points() + l_rug()

# Over-ride default layout
pl <- plotSlice(x = sm(v, 1), 
                fix = list("z" = seq(-2, 2, length.out = 9)), 
                a.facet = list(nrow = 2))
pl + l_fitRaster() + l_fitContour() + theme(panel.spacing = unit(0.5, "lines"))

### Example 2: plotting slices of 4D smooth
# Simulate data and fit GAM
n <- 5e3
x <- rnorm(n); y <- rnorm(n); z <- rnorm(n); z2 <- rnorm(n)
ob <- (x-z)^2 + (y-z)^2 + z2^3 + rnorm(n)
b <- bam(ob ~ s(x, y, z, z2), discrete = TRUE)
v <- getViz(b)

# Plot slices across "z" and "x"
pl <- plotSlice(x = sm(v, 1), 
                fix = list("z" = seq(-2, 2, length.out = 3), "x" = c(-1, 0, 1)))
pl + l_fitRaster() + l_fitContour() + l_points() + l_rug()

# Plot slices across "x", keeping "z" fixed
pl <- plotSlice(x = sm(v, 1), 
                fix = list("z" = 0, "x" = seq(-3, 3, length.out = 9)))
pl + l_fitRaster() + l_fitContour() + l_points() + l_rug()
}