connecting line like tree in r - r

Question

I have following type data for human family:
indvidual <- c("John", "Kris", "Peter", "King", "Marry", "Renu", "Kim", "Ken", "Lu")
Parent1 <- c( NA, NA, "John", "John", "John", NA, "Peter", NA, NA)
Parent2 <- c( NA, NA, "Kris", "Kris", "Renu", NA, "Lu", NA, NA)
X <- c( 2, 3, 2, 3, 4, 5, 1.5, 1, 1)
Y <- c( 3, 3, 2, 2, 2, 3, 1, 3, 2)
pchsize <- c( 4.5, 4.3, 9.2, 6.2, 3.2, 6.4, 2.1, 1.9, 8)
fillcol <- c( 8.5, 8.3, 1.2, 3.2, 8.2, 2.4, 2.6, 6.1, 3.2)
myd <- data.frame (indvidual, Parent1, Parent2, X, Y, pchsize,fillcol)
indvidual Parent1 Parent2 X Y pchsize fillcol
1 John <NA> <NA> 2.0 3 4.5 8.5
2 Kris <NA> <NA> 3.0 3 4.3 8.3
3 Peter John Kris 2.0 2 9.2 1.2
4 King John Kris 3.0 2 6.2 3.2
5 Marry John Renu 4.0 2 3.2 8.2
6 Renu <NA> <NA> 5.0 3 6.4 2.4
7 Kim Peter Lu 1.5 1 2.1 2.6
8 Ken <NA> <NA> 1.0 3 1.9 6.1
9 Lu <NA> <NA> 1.0 2 8.0 3.2
I want plot something like the following, individuals points are connected to parents (Preferably different line color to Parent1 and Parent2 listed). Also pch size and pch fill is scaled to other variables pchsize and fillcol. Thus plot outline is:
Here is my progress in ggplot2:
require(ggplot2)
ggplot(data=myd, aes(X, Y,fill = fillcol)) +
geom_point(aes(size = pchsize, fill = fillcol), pch = "O") +
geom_text(aes (label = indvidual, vjust=1.25))
Issues unsolved: connecting lines, making size of pch big and fill color at the sametime.

Answer 1

Here is ggplot2 solution
library(ggplot2)
individual <- c("John", "Kris", "Peter", "King", "Marry", "Renu", "Kim", "Ken", "Lu")
Parent1 <- c( NA, NA, "John", "John", "John", NA, "Peter", NA, NA)
Parent2 <- c( NA, NA, "Kris", "Kris", "Renu", NA, "Lu", NA, NA)
X <- c( 2, 3, 2, 3, 4, 5, 1.5, 1, 1)
Y <- c( 3, 3, 2, 2, 2, 3, 1, 3, 2)
pchsize <- c( 4.5, 4.3, 9.2, 6.2, 3.2, 6.4, 2.1, 1.9, 8)
fillcol <- c( 8.5, 8.3, 1.2, 3.2, 8.2, 2.4, 2.6, 6.1, 3.2)
myd <- data.frame (individual, Parent1, Parent2, X, Y, pchsize,fillcol)
SegmentParent1 <- merge(
myd[, c("individual", "X", "Y")],
myd[!is.na(myd$Parent1), c("Parent1", "X", "Y")],
by.x = "individual", by.y = "Parent1")
SegmentParent2 <- merge(
myd[, c("individual", "X", "Y")],
myd[!is.na(myd$Parent1), c("Parent2", "X", "Y")],
by.x = "individual", by.y = "Parent2")
Segments <- rbind(SegmentParent1, SegmentParent2)
ggplot(data=myd, aes(X, Y)) +
geom_segment(data = Segments, aes(x = X.x, xend = X.y, y = Y.x, yend = Y.y)) +
geom_point(aes(size = pchsize, colour = fillcol)) +
geom_text(aes (label = indvidual), vjust = 0.5, colour = "red", fontface = 2) +
scale_x_continuous("", expand = c(0, 0.6), breaks = NULL) +
scale_y_continuous("", expand = c(0, 0.4), breaks = NULL) +
scale_size(range = c(20, 40)) +
theme_bw()

Answer 2

Here is a solution just using plot(), text(), and arrows(). The for loop is a bit cluttered, but will work for larger data sets and it should be easy to play with the plot and arrows:
plot(myd$X,myd$Y, col='white', type="p", main="", ylab="", xlab="",
axes = FALSE, ylim = c(min(myd$Y)*.8, max(myd$Y)*1.2),
xlim = c(min(myd$X)*.8, max(myd$X)*1.2))
child = data.frame()
child = myd[!is.na(myd$Parent1),]
DArrows = matrix(0,nrow(child),4);
MArrows = matrix(0,nrow(child),4);
for (n in 1:nrow(child)){
d<-child[n,];
c1<-myd$indvidual==as.character(d$Parent1);
b1<-myd[t(c1)];
c2<-myd$indvidual==as.character(d$Parent2);
b2<-myd[t(c2)];
DArrows[n, 1]=as.double(d$X)
DArrows[n, 2]=as.double(d$Y)
DArrows[n, 3]=as.double(b1[4])
DArrows[n, 4]=as.double(b1[5])
MArrows[n, 1]=as.double(d$X)
MArrows[n, 2]=as.double(d$Y)
MArrows[n, 3]=as.double(b2[4])
MArrows[n, 4]=as.double(b2[5])
}
arrows(DArrows[,3],DArrows[,4],DArrows[,1],DArrows[,2],lwd= 2, col = "blue",length=".1")
arrows(MArrows[,3],MArrows[,4],MArrows[,1],MArrows[,2],lwd=2, col = "red",length=".1")
par(new=TRUE)
plot(myd$X,myd$Y,type = "p", main = "", ylab = "", xlab = "",cex = myd$pchsize,
axes = FALSE, pch = 21, ylim = c(min(myd$Y)*.8, max(myd$Y)*1.2),
xlim=c(min(myd$X)*.8, max(myd$X)*1.2), bg = myd$fillcol,fg = 'black')
text(1.12*myd$X, .85*myd$Y, myd$indvidual)
arrows((DArrows[,3]+DArrows[,1])/2, (DArrows[,4]+DArrows[,2])/2,
DArrows[,1], DArrows[,2], lwd = 2, col = "blue", length = ".1")
arrows((MArrows[,3]+MArrows[,1])/2, (MArrows[,4]+MArrows[,2])/2,
MArrows[,1], MArrows[,2], lwd = 2, col = "red", length = ".1")

Answer 3

One thing that jumped out to me was to treat this is a network - R has many packages to plot these.
Here's a very simple solution:
First, I used your parent list to make a sociomatrix - you can generally input networks using edge lists as well - here I put 1 for the first parental relationship and 2 for the second.
psmat <- rbind(c(0, 0, 1, 1, 1, 0, 0, 0, 0),
c(0, 0, 2, 2, 0, 0, 0, 0, 0),
c(0, 0, 0, 0, 0, 0, 1, 0, 0),
rep(0, 9),
rep(0, 9),
c(0, 0, 0, 0, 2, 0, 0, 0, 0),
rep(0, 9),
rep(0, 9),
c(0, 0, 0, 0, 0, 0, 2, 0, 0))
Then, using the network package I just hit:
require(network)
plot(network(psmat), coord = cbind(X, Y), vertex.cex = pchsize,
vertex.col = fillcol, label = indvidual, edge.col = psmat)
This isn't terribly pretty in itself, but I think gives you all the basic elements you wanted.
For the colors, I believe the decimal places are just rounded - I wasn't sure what to do with those.
I know I've seen people plot networks in ggplot, so that might give you a better result.
Edit:
So here's a really messy way of turning your data into a network object directly - someone else might be able to fix it. Additionally, I add an edge attribute (named 'P' for parental status) and give the first set a value of 1 and the second set a value of 2. This can be used when plotting to set the colors.
P1 <- match(Parent1, indvidual)
e1 <- cbind(P1, 1:9); e1 <- na.omit(e1); attr(e1, 'na.action') <- NULL
P2 <- match(Parent2, indvidual)
e2 <- cbind(P2, 1:9); e2 <- na.omit(e2); attr(e2, 'na.action') <- NULL
en1 <- network.initialize(9)
add.edges(en1, e1[,1], e1[,2])
set.edge.attribute(en1, 'P', 1)
add.edges(en1, e2[,1], e2[,2], names.eval = 'P', vals.eval = 2)
plot(en1, coord = cbind(X, Y), vertex.cex = pchsize,
vertex.col = fillcol, label = indvidual, edge.col = 'P')

Answer 4

Alternative solution use igraph
library(igraph)
mm<-data.frame(dest=c(as.character(myd$Parent1),as.character(myd$Parent2)))
mm$orig<-myd$individual
g<-graph.edgelist(as.matrix(mm[!is.na(mm$dest),]))
rownames(myd)<-as.character(myd[,1])
l<-as.matrix(myd[V(g)$name,4:5])
plot(g,layout=l,vertex.color=myd[V(g)$name,6],vertex.size=myd[V(g)$name,6])
Just play a bit with color a sizes!