Change colors in ggpairs now that params is deprecated

问题

I saw these posts GGally::ggpairs plot without gridlines when plotting correlation coefficient use ggpairs to create this plot

After reading I was able to implement this hack https://github.com/tonytonov/ggally/blob/master/R/gg-plots.r and my plot looks like this

I think this is a good result but I cannot change the colors.

A MWE is this

library(ggally)

# load the hack
source("ggally_mod.R") 
# I saved https://github.com/tonytonov/ggally/blob/master/R/gg-plots.r as "ggally_mod.R"
assignInNamespace("ggally_cor", ggally_cor, "GGally")

ggpairs(swiss)

Now I want to run

ggpairs(swiss, 
 lower=list(continuous="smooth", wrap=c(colour="blue")),
 diag=list(continuous="bar", wrap=c(colour="blue")))

But the colours remain the same. Is there a way to change the colours now that params is not working anymore?

回答1:

You are not using wrap correctly - see the vignette for details. Also for the diagonal you now have to use the function barDiag (but ggpairs gives very helpful errors to tell this)

So for your example, we can change the colour of the points in the lower panels and the fill of the bars below

library(GGally)
library(ggplot2)
ggpairs(swiss[1:3], 
        lower=list(continuous=wrap("smooth", colour="blue")),
        diag=list(continuous=wrap("barDiag", fill="blue")))

However, as the colour of the smooth is hard coded (see ggally_smooth), to change its colour you need to define you own function to pass. So from here

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"))),
                     diag=list(continuous=wrap("barDiag", fill="blue")))

In a similar way, here is a way to define a new upper correlation function (similar to what you have)

cor_fun <- function(data, mapping, method="pearson", ndp=2, sz=5, stars=TRUE, ...){

    x <- eval_data_col(data, mapping$x)
    y <- eval_data_col(data, mapping$y)

    corr <- cor.test(x, y, method=method)
    est <- corr$estimate
    lb.size <- sz* abs(est) 

    if(stars){
      stars <- c("***", "**", "*", "")[findInterval(corr$p.value, c(0, 0.001, 0.01, 0.05, 1))]
      lbl <- paste0(round(est, ndp), stars)
    }else{
      lbl <- round(est, ndp)
    }

    ggplot(data=data, mapping=mapping) + 
      annotate("text", x=mean(x, na.rm=TRUE), y=mean(y, na.rm=TRUE), label=lbl, size=lb.size,...)+
      theme(panel.grid = element_blank())
  }


ggpairs(swiss, 
        lower=list(continuous=wrap("smooth", colour="blue")),
        diag=list(continuous=wrap("barDiag", fill="blue")),
        upper=list(continuous=cor_fun))

回答2:

You can modify some parameters of GGally functions by using wrap() as explained here. But not all parameters are named for wrap to be useful. For example, if you try to change default palette with a manual colour scale within wrap you may get an error like Error in wrap("cor",…) all parameters must be named arguments. In that case you may build custom functions to generate any sort of ggplot object appropriate for the upper, lower or diagonal sections of the matrix plot.

However, there is a (safer) shortcut if you want to change some parameters (not named in GGally functions to be wrapped) without creating a custom function to design a ggplot object. You just call an already existing GGally function within a function call, adding the extra ggplot parameters. For example, to provide a manual scale colour for three categories (in the new column swiss$groups):

swiss$groups <- gl(n = 3, k = 1, length = nrow(swiss), labels = c("A", "B", "C"))

ggpairs(swiss, mapping = aes(colour = groups), columns = 1:6,
    upper = list(continuous = function(data, mapping, ...) {
         ggally_cor(data = data, mapping = mapping, size = 2) + scale_colour_manual(values = c("black", "dark green", "red"))}),
    lower = list(continuous = function(data, mapping, ...) {
         ggally_smooth(data = data, mapping = mapping, alpha = .2) + scale_colour_manual(values = c("black", "dark green", "red"))}),
    diag = list(continuous = function(data, mapping, ...) {
         ggally_barDiag(data = data, mapping = mapping, alpha = .5) + scale_fill_manual(values = c("black", "dark green", "red"))}))

来源：https://stackoverflow.com/questions/37889222/change-colors-in-ggpairs-now-that-params-is-deprecated

标签

plot

ggplot2

ggally