在R中获取连续线图

Question

I'd like to plot something like the image attached. It come from this paper http://www.nature.com/nature/journal/v488/n7410/extref/nature11319-s1.pdf (Figure 11D). I know it was done in R, but I don't know the package/function.

This is a subset of my data:

SampleID prevo.bact
37.TO.O -3.00468736
31.TO.V -3.42291741
06.BO.VG -2.56462361
37.PR.O  0.91296148
03.BA.O  0.02868464
30.BO.V -0.24479930

I ordered the values in crescent way and I tried to plot them using plot

mydata.ordered=order(my.data$prevo.bact) 
plot(my.data$prevo.bact[my.data.ordered])

This is quite close to the output I'd like to get, but I don't know how to change the points obtaining the vertical lines (no one of the types available in plot is like that) and how to change the color according to a class vector clD

clD = unlist(lapply(strsplit(row.names(my.data),'[.]'),function(x){x[[3]]}))
names(clD)=row.names(my.data)

Moreover, I don't want empty space between the points (like in the picture attached, I'd like a continuum). How can I get something similar? Probably the basic plot is not the way...

Thanks Francesca

Answer 1

I give it a try. I think the reason that the plot looks continuous is simply that there are enough points to create the illusion of continuity. In order to have enough points, I had to create some sample data myself, because the six points you give are not enough.

library(ggplot2)
my.data <- data.frame(SampleID=rep(c("37.TO.O","31.TO.V","06.BO.VG","37.PR.O","03.BA.O","30.BO.V"),times=30),
                  prevo.bact=rnorm(180,0,3),
                  stringsAsFactors=FALSE)
my.data$clD <- sapply(strsplit(my.data$SampleID,'[.]'),function(x){x[[3]]})
my.data.ordered <- my.data[order(my.data$prevo.bact),]
my.data.ordered$num <- 1:nrow(my.data)
ggplot(my.data.ordered,aes(num,prevo.bact)) + geom_point(size=5,shape="|",aes(col=clD)) + theme_classic()

I have used ggplot because I wouldn't know how to colour the data points using base graphics. The option shape="|" uses vertical lines instead of points.

This is the figure I get: