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I want to start by saying that I am a novice user of R and especially of this website, so if it is necessary that I clarify anything here, please let me know! I don't quite understand everything yet, so please feel free to "dumb down" as possible.

Question: I want to create PCA graphs depicting two groups (in this case species). I also want to draw ellipses or frames around them.

Thankfully I have accomplished this task using ggplot2! However, I am not able to change the colors of the points or ellipses/frames beyond the defaults.

Can you please offer some assistance on this matter?

Please see example code below, which is just the traditional iris data set often used in PCA examples.

###load in plackages###
library(ggbiplot)
library(ggfortify)
library(cluster)

#my actual data is very similar to the iris data, though in my data the     "Species" column is first
head(iris)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1          5.1         3.5          1.4         0.2  setosa
2          4.9         3.0          1.4         0.2  setosa
3          4.7         3.2          1.3         0.2  setosa
4          4.6         3.1          1.5         0.2  setosa
5          5.0         3.6          1.4         0.2  setosa
6          5.4         3.9          1.7         0.4  setosa
df <- iris[c(1, 2, 3, 4)]
autoplot(prcomp(df))
autoplot(prcomp(df), data = iris, colour = 'Species') #pca graph with   species depicted in different colors

PCA GRAPH OF SPECIES DEPICTED IN DIFFERENT COLORS

autoplot(prcomp(df), data = iris, colour = 'Species', shape='Species', frame=T)

PCA GRAPH WITH FRAMES AROUND POINTS

zx8754
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Alannie-Grace Grant
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    I can't install ggbiplot right now but have you tried to pass scale_color_manual( your 3 custom values here) ? – Matias Andina Nov 10 '15 at 22:53
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    And `scale_fill_manual` for the frames. Lots of examples around for ggplot2, just search for, e.g., "ggplot2 manually set colors". You might edit your question to make it clear that the code you include relies on *ggfortify* and not either of the other packages (as far as I can tell). – aosmith Nov 10 '15 at 22:56
  • Thanks @aosmith! This suggestion you gave was perfect! I posted the solution I came to below. – Alannie-Grace Grant Nov 11 '15 at 02:12

2 Answers2

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I have made the same PCA

data<-iris
df<-iris[c(1, 2, 3, 4)]
PC<-prcomp(df)
PCi<-data.frame(PC$x,Species=data$Species)

Now you do the normal plot and change ggplot parameters as usual

ggplot(PCi,aes(x=PC1,y=PC2,col=Species))+
   geom_point(size=3,alpha=0.5)+ #Size and alpha just for fun
   scale_color_manual(values = c("#FF1BB3","#A7FF5B","#99554D"))+ #your colors here
   theme_classic()

enter image description here

Also, check scale_fill_manual for the frame

EDIT

I thought that adding a frame should be easier, check here https://stats.stackexchange.com/questions/22805/how-to-draw-neat-polygons-around-scatterplot-regions-in-ggplot2
and here ggplot2: geom_polygon with no fill

Also, I still believe that ggbiplot should handle scale_color_manual and scale_fill_manual, could you update your question that fails?

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Matias Andina
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  • I thought that adding a frame should be easier, check here http://stats.stackexchange.com/questions/22805/how-to-draw-neat-polygons-around-scatterplot-regions-in-ggplot2 – Matias Andina Nov 10 '15 at 23:30
  • Thanks @Matias! I have your used suggestions `scale_ color_manual` and `scale_fill_manual` for my solution. This was exactly what I needed! – Alannie-Grace Grant Nov 11 '15 at 02:09
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Awesome sauce!

The answer wasn't quite hidden in those examples but I found scale_color_manual and scale_fill_manual to hold exactly what I desired: to change the frames to any color imaginable! 

#using autoplot from earlier, I placed it into an object
a<-autoplot(prcomp(df), data = iris, colour = 'Species', shape='Species', frame=T)
#then I added on scale_color_manual and scale_fill_manual with the wacky color combos that would never be publishable 
a + scale_fill_manual(values = c("#FF1BB3","#A7FF5B","#99554D")) + scale_color_manual(values = c("black","white","orange"))

PCA GRAPH WITH DIFFERENT COLORS

Thanks so much for the help! Very grateful to have this little (or rather exceptionally large) group here!

Alannie-Grace Grant
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