Multidimensional scaling plot in R - r

Question

I have a dataset ("data") that looks like this:
PatientID Visit Var1 Var2 Var3 Var4 Var5
1 ID1 0 44.28 4.57 23.56 4.36 8.87
2 ID1 1 58.60 5.34 4.74 3.76 6.96
3 ID1 2 72.44 11.18 21.22 2.15 8.34
4 ID2 0 65.98 6.91 8.57 1.19 7.39
5 ID2 1 10.33 38.27 0.48 14.41 NA
6 ID2 2 69.45 11.18 20.69 2.15 8.34
7 ID3 0 69.16 6.17 10.98 1.91 6.12
8 ID3 1 86.02 3.28 16.29 4.28 5.74
9 ID3 2 69.45 NA 20.69 2.15 8.34
10 ID4 0 98.55 26.75 2.89 3.92 2.19
11 ID4 1 32.66 14.38 4.96 1.13 4.78
12 ID4 2 70.45 11.42 21.78 2.15 8.34
I need to to generate an MDS plot with all datapoints. I also need the visit-points to be linked by a line and coloured as green for visit 1, red for visit 2 and black for visit3 (consistent colours for all individuals).
My code looks like this (quite lenghty, but it doesn't work):
data.cor <- cor(t(data[,3:7]), use = "pairwise.complete.obs", method = "spearman")
dim(data.cor)
dim(data)
rownames(data.cor) <- paste0(data$PatientID, "V", data$Visit)
colnames(data.cor) <- paste0(data$PatientID, "V", data$Visit)
c <- dist(data.cor)
fit <- cmdscale(c,eig=TRUE, k=2)
ff <- fit$points
ff <- as.data.frame(ff)
ff$pair <- paste0(substr(rownames(ff),1,6))
ff$pair <- factor(ff$pair)
pc.pair.distances <- matrix(nrow = nlevels(ff$pair), ncol = 1)
for(i in 1:nlevels(ff$pair)){
pair2 <- ff[ff$pair %in% levels(ff$pair)[i] , ]
pc.pair.distances[i,1] <- sqrt(
((pair2[1,1] - pair2[2,1]) * (pair2[1,1] - pair2[2,1]))
+ ((pair2[1,2] - pair2[2,2]) * (pair2[1,2] - pair2[2,2]))
)
rm(pair2)
}
plot(ff[,1], ff[,2], xlab="Principal 1", ylab="Principal 2", type = "n", las = 1)
for(i in 1:nlevels(ff$pair)){
lines(ff[ff$pair == levels(ff$pair)[i],1], ff[ff$pair == levels(ff$pair)[i],2], col = "grey")
}
points(ff[,1], ff[,2], xlab="Coordinate 1", ylab="Coordinate 2", type = "p",
pch = ifelse(grepl(x = substr(rownames(ff), 7,8), "V1"), 20, 18),
cex = 1.3)
)
I would really appreciate your help.

Answer 1

I suggest you to modify your data.frame in order to add a column for visit number and for indiv id with the function sapply.
ff$visit <- sapply(ff$pair,function(x){substr(x,5,5)})
ff$indiv <- sapply(ff$pair,function(x){substr(x,3,3)})
And then the library ggplot2 is very usefull to plot data. First, you draw the points :
g <- ggplot(ff,aes(V1,V2))+geom_point(aes(color=visit))
And then add lines for each individual :
for (i in unique(ff$indiv)){
g <- g+geom_line(data=ff[ff$indiv==i,],aes(V1,V2))
}