I have two scatterplots, based on different but related data, created using qplot() from ggplot2. (Learning ggplot hasn't been a priority because qplot has been sufficient for my needs up to now). What I want to do is superimpose/overlay the two charts so that the x,y data for each is plotted in the same plot space. The complication is that I want each plot to retain its formatting/aesthetics.
That data in question are row and column scores from correspondence analysis - corresp() from MASS - so the number of data rows (i.e. samples or taxa) differ between the two datasets. I can plot the two score sets together easily. Either by combing the two datasets or, even easier, just using the biplot() function.
However, I have been using qplot to get the plots looking exactly as I need them; with samples plotted as colour-coded symbols and taxa as labels:
PlotSample <- qplot(DataCorresp$rscore[,1], DataCorresp$rscore[,2],
colour=factor(DataAll$ColourCode)) +
scale_colour_manual(values = c("black","darkgoldenrod2",
"deepskyblue2","deeppink2"))
and
PlotTaxa <- qplot(DataCorresp$cscore[,1], DataCorresp$cscore[,2],
label=colnames(DataCorresp), size=10, geom=“text”)
Can anyone suggest a way by which either
- the two plots (
PlotSampleandPlotTaxa) can be superimposed atop of each other, - the two datasets (
DataCorresp$rscoreandDataCorresp$cscore) can be plotted together but formatted in their different ways, or - another function (e.g.
biplot()) that could be used to achieve my aim.
Example of workflow using a extremely simplified and made-up dataset:
> require(MASS)
> require(ggplot2)
> alldata<-read.csv("Fake data.csv",header=T,row.name=1)
> selectdata<-alldata[,2:10]
> alldata
Period Species.1 Species.2 Species.3 Species.4 Species.5 Species.6
Sample-1 Early 50 87 97 12 60 49
Sample-2 Early 41 90 36 52 36 27
Sample-3 Early 87 56 82 45 56 13
Sample-4 Early 37 47 78 29 53 34
Sample-5 Early 58 70 34 35 8 21
Sample-6 Early 94 82 48 16 27 26
Sample-7 Early 91 69 50 57 24 13
Sample-8 Early 63 38 86 20 28 11
Sample-9 Middle 4 19 55 99 86 38
Sample-10 Middle 29 25 10 93 37 54
Sample-11 Middle 48 12 59 73 39 92
Sample-12 Middle 31 6 34 81 39 54
Sample-13 Middle 29 40 26 52 34 84
Sample-14 Middle 1 46 15 97 67 41
Sample-15 Late 43 47 30 18 60 23
Sample-16 Late 45 10 49 2 2 45
Sample-17 Late 14 8 51 36 58 51
Sample-18 Late 41 51 32 47 23 43
Sample-19 Late 43 17 6 54 4 12
Sample-20 Late 20 25 1 29 35 2
Species.7 Species.8 Species.9
Sample-1 41 39 57
Sample-2 59 4 45
Sample-3 10 56 5
Sample-4 59 30 39
Sample-5 9 29 57
Sample-6 29 24 35
Sample-7 22 4 42
Sample-8 31 19 40
Sample-9 17 7 57
Sample-10 6 9 29
Sample-11 34 20 0
Sample-12 56 41 59
Sample-13 6 31 13
Sample-14 25 12 28
Sample-15 60 75 84
Sample-16 32 69 34
Sample-17 48 53 56
Sample-18 80 86 46
Sample-19 50 70 82
Sample-20 57 84 70
> biplot(selectca,cex=c(0.6,0.6))
> selectca<-corresp(selectdata,nf=5)
> PlotSample <- qplot(selectca$rscore[,1], selectca$rscore[,2], colour=factor(alldata$Period) )
> PlotTaxa<-qplot(selectca$cscore[,1], selectca$cscore[,2], label=colnames(selectdata), size=10, geom="text")
The biplot will produce this plot: /r/10wk1a8/5
The PlotSample appears as such: /r/i29cba/5
The PlotTaxa appears as such: /r/245bl9d/5
EDIT so don't have enough rep to post pictures and tinypic links not accepted (despite https://meta.stackexchange.com/questions/60563/how-to-upload-images-on-stack-overflow). So if you add tinypic's URL to the start of those codes above you'll get there.
Essentially I want to creat the biplot plot but with samples colour coded as they are in PlotSample.
