R: Changing the Color of Overlapping Points

Question

I am working with the R programming language. I made the following graph that shows a scatterplot between points of two different colors :

library(ggplot2)


a = rnorm(10000,10,10)
b = rnorm(10000, 10, 10)
c = as.factor("red")

data_1 = data.frame(a,b,c)

a = rnorm(10000,7,5)
b = rnorm(10000, 7, 5)
c = as.factor("blue")

data_2 = data.frame(a,b,c)

final = rbind(data_1, data_2)

my_plot = ggplot(final, aes(x=a, y=b, col = c)) + geom_point() +  theme(legend.position="top") + ggtitle("My Plot")

My Question: Is there a way to "change the colors of overlapping points"?

Here is what I tried so far:

1) I found the following question (Visualizing two or more data points where they overlap (ggplot R)) and tried the strategy suggested:

linecolors <- c("#714C02", "#01587A", "#024E37")
fillcolors <- c("#9D6C06", "#077DAA", "#026D4E")

# partially transparent points by setting `alpha = 0.5`
ggplot(final, aes(a,b, colour = c, fill = c)) +
  geom_point(alpha = 0.5) +
  scale_color_manual(values=linecolors) +
  scale_fill_manual(values=fillcolors) +
  theme_bw()

This shows the two different colors along with the overlap, but it is quite dark and still not clear. Is there a way to pick better colors/resolutions for this?

2) I found the following link which shows how to make color gradients for continuous variables : https://drsimonj.svbtle.com/pretty-scatter-plots-with-ggplot2 - but I have discrete colors and I do not know how to apply this

3) I found this question over here (Any way to make plot points in scatterplot more transparent in R?) which shows to do this with the base R plot, but not with ggplot2:

addTrans <- function(color,trans)
{
  # This function adds transparancy to a color.
  # Define transparancy with an integer between 0 and 255
  # 0 being fully transparant and 255 being fully visable
  # Works with either color and trans a vector of equal length,
  # or one of the two of length 1.

  if (length(color)!=length(trans)&!any(c(length(color),length(trans))==1)) stop("Vector lengths not correct")
  if (length(color)==1 & length(trans)>1) color <- rep(color,length(trans))
  if (length(trans)==1 & length(color)>1) trans <- rep(trans,length(color))

  num2hex <- function(x)
  {
    hex <- unlist(strsplit("0123456789ABCDEF",split=""))
    return(paste(hex[(x-x%%16)/16+1],hex[x%%16+1],sep=""))
  }
  rgb <- rbind(col2rgb(color),trans)
  res <- paste("#",apply(apply(rgb,2,num2hex),2,paste,collapse=""),sep="")
  return(res)
}


cols <- sample(c("red","green","pink"),100,TRUE)


# Very transparant:
plot(final$a , final$b ,col=addTrans(cols,100),pch=16,cex=1)

But this is also not able to differentiate between the two color classes that I have.

Problem: Can someone please suggest how to fix the problem with overlapping points, such that the overlap appear more visible?

Thanks!

This is not what you're looking for but would it make ense to plot histograms/desnity plots for the x and y-axis to illustrate the overlap? — JAQuent, Dec 08 '21 at 04:59
@ JAQuent: Thank you for your reply! I considered histograms in the past - however, I trying to show individual points was hoping to do this with a histogram. I will keep looking for a way to do this! Thank you! — stats_noob, Dec 08 '21 at 05:02
sounds like the ggpointdensity package might be useful to you. It’s quite slow in plotting, but makes nice visual effects. https://github.com/LKremer/ggpointdensity — tjebo, Dec 08 '21 at 07:48
also, please check this thread, I think it has some nice ideas for dealing with lots of data points https://stackoverflow.com/questions/7714677/scatterplot-with-too-many-points — tjebo, Dec 08 '21 at 07:50

Rfanatic · Answer 1 · 2021-12-08T07:58:51.383

I would use a density heatmap

ggplot(final, aes(x=a, y=b, col = c))+
    stat_density_2d(aes(fill = stat(density)), geom = 'raster', contour = FALSE) +       
      scale_fill_viridis_c() +
      coord_cartesian(expand = FALSE) +
      geom_point(shape = '.', col = 'white')

or

ggplot(final, aes(x=a, y=b, col = c))+
stat_density_2d(aes(fill = stat(level)), geom = 'polygon') +
  scale_fill_viridis_c(name = "density") +
  geom_point(shape = '.')

or

ggplot(final, aes(x=a, y=b, col = c))+
  geom_point(alpha = 0.1) +
  geom_rug(alpha = 0.01)

R: Changing the Color of Overlapping Points

1 Answers1