how to improve PCA visualization using ggplot?

Question

[mthm]

I have used this piece of script to draw the PCA based on eigenvalue and eigenvector

percentage <- round((eigenval/(sum(eigenval))*100), 2)
percentage <- as.matrix(percentage)
percentage <- paste0(names(percentage), " (", percentage, "%)")
Names <- c ("mn27hd", "mdkk987", "mnsdnu83", "sjednu83", "bjeo972s")
pop.colour <- c("blue", "red", "green", "orange", "brown")
ggplot(eigenvec, aes(x=PC1, y=PC2, colour=pop.colour, label=Names)) +
    geom_point(size=3) + geom_text(aes(label=Names), hjust=0, vjust=-0.5) + xlab(percentage[1]) + ylab(percentage[2])

how can I:

1. change the xlab and ylab names to show as: PC1 (36.61%), PC2 (33.7%)?

2. move only the pink label slightly left-side cause when I do it generally then the two left labels go outside the image or too close to the edge?

3. change the legend name and categories from the colour to the population name?

Answer 1

[Sam]

I like to use labs instead of xlab and ylab and add the information to the data.frame directly. Do you only have 4 data point and you are certain that the name are corresponding to the correct PC value? If so do

percentage <- round((eigenval/(sum(eigenval))*100), 2)
percentage <- as.matrix(percentage)
percentage <- paste0(names(percentage), " (", percentage, "%)")
eigenvec$Pop <- c ("mn27hd", "mdkk987", "mnsdnu83", "sjednu83", "bjeo972s")

pop.colour <- c("blue", "red", "green", "orange", "brown")
ggplot(eigenvec, aes(x=PC1, y=PC2, colour=Pop, label=Pop)) +
    geom_point(size=3) + geom_text(hjust=-0.1, vjust=-0.5) +
    scale_color_manual(values = pop.colour) + 
    labs(x=paste0("PC1 (",percentage[1],")"), y= paste0("PC2 (",percentage[2], ")"), color = "Population")

I don't know have mock data to play with so there might be bug to the code. You can modify hjust in geom_text to adjust the horizontal shift

[mthm]

Thanks the legend worked. the PC1 and PC2 axes didn't! it says:

Error in "PC1 (" + percentage[1] : 
  non-numeric argument to binary operator

that is how my percentage looks like

> percentage
[1] " (36.61%)" " (33.7%)"  " (19.75%)" " (18.03%)" " (-0.1%)"

I can only adjust the hjust=0.4 without throwing the two green and blue labels out of the graph! which is still not enough for the purple label to be fully in! I was thinking if it is possible to change the dimensions of the graph so that labels fit in?

[Sam]

My bad, should have used , instead of +. Have now fixed that.

If you don't mind installing an additional package, I found ggrepel really useful in this scenario. You can find examples here

[mthm]

Great, fixed the label with this and worked fine (x=paste0("PC1" ,percentage[1]), y= paste0("PC2" ,percentage[2])