Suppose I would like to produce a kind of tree structure like the one below:
plot(0, type="n",xlim=c(0, 5), ylim=c(-3, 8), axes=FALSE, xlab="", ylab="", main="")
points(1, 2.5)
points(3, 5)
points(3, 0)
lines(c(1, 3), c(2.5, 5))
lines(c(1, 3), c(2.5, 0))
text(1, 2.5, adj=1, label="Parent ")
text(3, 5, adj=0, label=" Child 1")
text(3, 0, adj=0, label=" Child 2")
I wonder if there is a way in R
where we can produce curved lines that resemble varying degrees of a S-curve like the ones below. Crucially it would be great if it would be possible to create such lines without resorting to ggplot
.
EDIT removed and made into an answer
Following @thelatemail's suggestion, I decided to make my edit into an answer. My solution is based on @thelatemail's answer.
I wrote a small function to draw curves, which makes use of the logistic function:
#Create the function
curveMaker <- function(x1, y1, x2, y2, ...){
curve( plogis( x, scale = 0.08, loc = (x1 + x2) /2 ) * (y2-y1) + y1,
x1, x2, add = TRUE, ...)
}
A working example is below. In this example, I want to create a plot for a taxonomy with 3 levels: parent
--> 2 children
-- > 20 grandchildren
. One child has 12 grandchildren, and the other child has 8 children.
#Prepare data:
parent <- c(1, 16)
children <- cbind(2, c(8, 28))
grandchildren <- cbind(3, (1:20)*2-1)
labels <- c("Parent ", paste("Child ", 1:2), paste(" Grandchild", 1:20) )
#Make a blank plot canvas
plot(0, type="n", ann = FALSE, xlim = c( 0.5, 3.5 ), ylim = c( 0.5, 39.5 ), axes = FALSE )
#Plot curves
#Parent and children
invisible( mapply( curveMaker,
x1 = parent[ 1 ],
y1 = parent[ 2 ],
x2 = children[ , 1 ],
y2 = children[ , 2 ],
col = gray( 0.6, alpha = 0.6 ), lwd = 1.5 ) )
#Children and grandchildren
invisible( mapply( curveMaker,
x1 = children[ 1, 1 ],
y1 = children[ 1, 2 ],
x2 = grandchildren[ 1:8 , 1 ],
y2 = grandchildren[ 1:8, 2 ],
col = gray( 0.6, alpha = 0.6 ), lwd = 1.5 ) )
invisible( mapply( curveMaker,
x1 = children[ 2, 1 ],
y1 = children[ 2, 2 ],
x2 = grandchildren[ 9:20 , 1 ],
y2 = grandchildren[ 9:20, 2 ],
col = gray( 0.6, alpha = 0.6 ), lwd = 1.5 ) )
#Plot text
text( x = c(parent[1], children[,1], grandchildren[,1]),
y = c(parent[2], children[,2], grandchildren[,2]),
labels = labels,
pos = rep(c(2, 4), c(3, 20) ) )
#Plot points
points( x = c(parent[1], children[,1], grandchildren[,1]),
y = c(parent[2], children[,2], grandchildren[,2]),
pch = 21, bg = "white", col="#3182bd", lwd=2.5, cex=1)
Sounds like a sigmoid curve, e.g.:
f <- function(x,s) s/(1 + exp(-x))
curve(f(x,s=1),xlim=c(-4,4))
curve(f(x,s=0.9),xlim=c(-4,4),add=TRUE)
curve(f(x,s=0.8),xlim=c(-4,4),add=TRUE)
curve(f(x,s=0.7),xlim=c(-4,4),add=TRUE)
Result:
You can start to adapt this, e.g. here's a clunky bit of code:
plot(NA,type="n",ann=FALSE,axes=FALSE,xlim=c(-6,6),ylim=c(0,1))
curve(f(x,s=1),xlim=c(-4,4),add=TRUE)
curve(f(x,s=0.8),xlim=c(-4,4),add=TRUE)
curve(f(x,s=0.6),xlim=c(-4,4),add=TRUE)
text(
c(-4,rep(4,3)),
c(0,f(c(4),c(1,0.8,0.6))),
labels=c("Parent","Kid 1","Kid 2","Kid 3"),
pos=c(2,4,4,4)
)
Result:
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