1

I've used ggbiplot to produce a biplot. I want points of different colours for different factor levels and the size of points to represent sample size. The problem that's driving me nuts is that part of the size vector c(1,2,2,1,3,2,2,1,3,3,2,1,1,1,2,3,2,2,3,1 is printed in the legend:

enter image description here

I used:

library(ggbiplot)
pplot <- function(pcaMatrix, cultures, sample.size = NA, FIRST=1, SECOND=2, ELLIPSE.PROB=0.68, SCALE = FALSE, LABELS=NULL){
  PCA <- prcomp(na.omit(pcaMatrix), scale. = SCALE)
  plot <- ggbiplot(PCA, obs.scale = 1, var.scale = 1, labels=LABELS, ellipse = {Ellipse.prob>0}, groups=cultures, circle = FALSE, choices=c(FIRST,SECOND), ellipse.prob=ELLIPSE.PROB)
  plot <- plot + geom_point(aes_string(colour=cultures, size = sample.size)) #+ scale_size_identity() 
  plot <- plot + scale_color_discrete(name = '')
  plot <- plot + scale_size_continuous(labels = c("200+", "500+", "1000+", "2000+", "4000+"))
  plot <- plot + theme(legend.direction = 'horizontal', legend.position = 'top')
  plot <- plot + theme(aspect.ratio=1)
  print(plot)
}

pplot(grav, grav.cultures, grav.sample, 1,2, ELLIPSE.PROB=0)

where 

> head(grav)
      Microlithisme Substrat     BpBG Crans  Gm   PD   F
    1          25.0     29.9 61.94226   0.5 0.3 27.0 0.3
    2          44.8     29.3 20.93023   2.1 0.0 47.9 0.0
    3           7.0     66.2 57.58929   0.5 0.2  5.8 0.2
    4          13.2     12.9 55.41126   6.6 0.0 40.0 0.2
    5           2.0      9.0 75.03045   0.1 0.0  6.9 0.0
    6          16.4     17.3 51.36519   0.9 0.2 20.9 0.1

> head(grav.cultures)
[1] GR GR GR GR GR GR
Levels:  AUR AZI EG EGL GR GR.Italy MAG SOL

The actual sample size is modified to control manually the size of points: 

> head(grav.sample)
[1]  360  986  599  457 1222  899

grav.sample[grav.sample>=200 & grav.sample < 500] <- 1
grav.sample[grav.sample>=500 & grav.sample<1000] <- 2
grav.sample[grav.sample>=1000 & grav.sample<2000] <- 3
grav.sample[grav.sample>=2000 & grav.sample<4000] <- 4
grav.sample[grav.sample>=4000 & grav.sample<8000] <- 5

> head(grav.sample)
[1] 1 2 2 1 3 2

I really just can't figure this one out. Why is part of the size vector printing in my legend?

Pertinax
  • 417
  • 4
  • 17
  • 4
    Have you tried changing the name of the legend title through `scale_size_continuous(name = "My title", ...)`? – Roman Luštrik May 13 '17 at 15:59
  • @Roman That worked, I just used `scale_size_continuous(name="", ...)`, excellent! Do you know why it was improvising a name? – Pertinax May 13 '17 at 16:03
  • 3
    You got the `deparse`-d version of an argument that had no name. Try: `deparse( c(1,2,3) )` – IRTFM May 13 '17 at 16:54

0 Answers0