How to use loess method in GGally::ggpairs using wrap function
I am trying to replicate this simple example given in the Coursera R Regression Models course:
require(datasets)
data(swiss)
require(GGally)
require(ggplot2)
ggpairs(swiss, lower = list(continuous = "smooth", params = c(method = "loess")))
I expect to see a 6x6 pairs plot - one scatterplot with loess smoother and confidence intervals for each combination of the 6 variables in the swiss data.
However, I get the following error:
Error in display_param_error() : 'params' is a deprecated argument. Please 'wrap' the function to supply arguments. help("wrap", package = "GGally")
I looked through the ggpairs() and wrap() help files and have tried lots of permutations of the wrap() and wrap_fn_with_param_arg() functions.
I can get this to work as expected:
ggpairs(swiss, lower = list(continuous = wrap("smooth")))
But once I add the loess part in, it does not:
ggpairs(swiss, lower = list(continuous = wrap("smooth"), method = wrap("loess")))
I get this error when I tried the line above.
Error in value[3L] : The following ggpair plot functions are readily available: continuous: c('points', 'smooth', 'density', 'cor', 'blank') combo: c('box', 'dot', 'facethist', 'facetdensity', 'denstrip', 'blank') discrete: c('ratio', 'facetbar', 'blank') na: c('na', 'blank')
diag continuous: c('densityDiag', 'barDiag', 'blankDiag') diag discrete: c('barDiag', 'blankDiag') diag na: c('naDiag', 'blankDiag')
You may also provide your own function that follows the api of function(data, mapping, ...){ . . . } and returns a ggplot2 plot object Ex: my_fn <- function(data, mapping, ...){ p <- ggplot(data = data, mapping = mapping) + geom_point(...) p } ggpairs(data, lower = list(continuous = my_fn))
Function provided: loess
Obviously I am entering loess in the wrong place. Can anyone help me understand how to add the loess part in?
Note that my problem is different to this one, as I am asking how to implement loess in ggpairs since the params argument became deprecated.
Thanks very much.
One quick way is to write your own function... the one below was edited from the one provided by the ggpairs error message in your question
library(GGally)
library(ggplot2)
data(swiss)
# Function to return points and geom_smooth
# allow for the method to be changed
my_fn <- function(data, mapping, method="loess", ...){
p <- ggplot(data = data, mapping = mapping) +
geom_point() +
geom_smooth(method=method, ...)
p
}
# Default loess curve
ggpairs(swiss[1:4], lower = list(continuous = my_fn))
# Use wrap to add further arguments; change method to lm
ggpairs(swiss[1:4], lower = list(continuous = wrap(my_fn, method="lm")))
This perhaps gives a bit more control over the arguments that are passed to each geon_
my_fn <- function(data, mapping, pts=list(), smt=list(), ...){
ggplot(data = data, mapping = mapping, ...) +
do.call(geom_point, pts) +
do.call(geom_smooth, smt)
}
# Plot
ggpairs(swiss[1:4],
lower = list(continuous =
wrap(my_fn,
pts=list(size=2, colour="red"),
smt=list(method="lm", se=F, size=5, colour="blue"))))
Maybe you are taking the Coursera online course Regression Models and try to convert the Rmarkdown file given by the course to html file, and come across this error as I do.
The way I tried out is:
require(datasets); data(swiss); require(GGally); require(ggplot2)
g = ggpairs(swiss, lower = list(continuous = wrap("smooth", method = "lm")))
g
Also you can try using method="loess" , but the outcome looks a bit different from that given in the lecture. method = "lm" may be a better fit as I see.
I suspected as well you were taking Coursera's class. Though, I could not find any github repo containing ggplot's examples.
Here's what I did to make it work:
gp = ggpairs(swiss, lower = list(continuous = "smooth"))
gp