How to use loess method in GGally::ggpairs using wrap function

Question

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.

user20650 · Accepted Answer · 2016-01-30T12:53:46.250

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"))))

@Ben; if you want to split each plot by factor you can just use `ggpairs` functionality e.g. `ggpairs(iris, aes(col=Species), lower = list(continuous = my_fn)) `. If you want to restrict it to specific plots then you will need to extend the `my_fn` function. here are a couple of recent q and a's which should help; https://stackoverflow.com/questions/66246984/how-to-customize-graph-with-2nd-correlation-line-in-ggpairs/66248574#66248574, or even split by group. https://stackoverflow.com/questions/71082421/tweaking-ggpairs-or-a-better-solution-to-a-correlation-matrix/71131736#71131736 ; — user20650, Apr 21 '22 at 14:50

score 13 · Answer 2 · edited Aug 12 '16 at 09:18

13

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.

edited Aug 12 '16 at 09:18

loki

9,816
7
56
82

answered Aug 12 '16 at 08:42

scarain

191
2
2

Thanks for suggesting this, but when I try your code, I get an error Error: Unknown parameters: method – meenaparam Aug 15 '16 at 19:26
1

@meenaparam In my case I've got no errors. Some `R.version` output: _platform_ `x86_64-pc-linux-gnu`, _os_ `linux-gnu`, _version.string_ `R version 3.3.3 (2017-03-06)`. – Cryptor Apr 04 '17 at 09:08
1

This does work for me now, they must have updated `ggally`, thanks! – meenaparam Jun 18 '17 at 19:33
Is it possible at all to set alpha for the SE? – Adel Aug 13 '21 at 05:11
I have run the following code without any issue for a while. All of a sudden I am getting an error message. I have not updated myself with any recent updates in the package that could lead to this issue. Here is the code `ggpairs(df, columns = c(2:5, 14), lower = list(continuous = wrap("smooth", method = "lm")), )`. The error message is as follows: Error in wrap("smooth", method = "lm") : unused argument (method = "lm"). Can anyone shed some light as to what I am doing wrong here? – Tathagato Sep 14 '22 at 02:00

score 2 · Answer 3 · answered Jun 18 '17 at 15:20

2

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

answered Jun 18 '17 at 15:20

Firefighter1017

86
1
9

Thanks @Firefighter1017, but this gives an linear fit (`lm`) rather than a loess smoother as I wanted. See @scarain's answer above to make your code work. – meenaparam Jun 18 '17 at 19:34

score 0 · Answer 4 · answered Jul 21 '22 at 17:51

0

This works: ggpairs(swiss, lower = list(continuous = wrap("smooth", method = "loess")))

answered Jul 21 '22 at 17:51

Murali

13
5

How to use loess method in GGally::ggpairs using wrap function

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