CODEWITHSUNDEEP
rggplot2ellipse
RB88
RB88

Reputation: 167

ggplot2 & stat_ellipse: Draw ellipses around multiple groups of points

This might be a simple one, but I'm trying to draw ellipses around my treatments on my PCoA plot.

My data frame (sc) is:

             MDS1        MDS2 Treatment
X1xF1 -0.19736183 -0.24299825   1xFlood
X1xF2 -0.17409568 -0.29727596   1xFlood
X1xF3 -0.15272444 -0.28553837   1xFlood
S1    -0.06643271  0.47049959     Start
S2    -0.15143350  0.31152966     Start
S3    -0.26156297  0.12296849     Start
X3xF1  0.29840827  0.04581617  3xFloods
X3xF2  0.50503749 -0.07011503  3xFloods
X3xF3  0.20016537 -0.05488630  3xFloods

and my code is:

ggplot(data=sc,(aes(x=MDS1,y=MDS2,colour = Treatment)))+geom_point(size=3)+
  ggtitle("PCoA of samples at 'class' level(method='Bray')\n",sep=''))+
  theme_bw()+guides(colour = guide_legend(override.aes = list(size=3)))+
  stat_ellipse()

It plots the PCoA okay up until stat_ellipse(). I've tried it with various parameters and at best I can get one ellipse for the whole plot (although I can't seem to reproduce that now).

What I'm after is three CI ellipses for the three treatments, coloured the same as the treatments. Any help would be very appreciated!

Thanks.

Upvotes: 2

Views: 13896

Answers (1)

jlhoward
jlhoward

Reputation: 59345

There is no stat_ellipse(...) in the ggplot package, so you must have retreived it from somewhere else. Care to share?? There are at least two versions that I am aware of, here, and here. Neither of these seem to work with your dataset, which is odd because both have worked with other datasets.

I finally fell back on the option of generating the ellipses externally to ggplot, which is not that difficult really.

library(ggplot2)
library(ellipse)
centroids <- aggregate(cbind(MDS1,MDS2)~Treatment,sc,mean)
conf.rgn  <- do.call(rbind,lapply(unique(sc$Treatment),function(t)
  data.frame(Treatment=as.character(t),
             ellipse(cov(sc[sc$Treatment==t,1:2]),
                     centre=as.matrix(centroids[t,2:3]),
                     level=0.95),
             stringsAsFactors=FALSE)))

ggplot(data=sc,(aes(x=MDS1,y=MDS2,colour = Treatment)))+
  geom_point(size=3)+
  geom_path(data=conf.rgn)+
  ggtitle(paste("PCoA of samples at 'class' level(method='Bray')\n",sep=''))+
  theme_bw()+
  guides(colour = guide_legend(override.aes = list(size=3)))

Upvotes: 8

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