The two functions below will see if the current graphics device appears to
contain a dendrogram plot, and if so will return the substree when a user
clicks on a node. Note: function name identify.dendrogram allows the
dendrogram class to bind this function for identify(dnd). If someone wants to
incorporate this into the public dendrogram distribution, please feel free to
do so.
David
Example:
# plot a dendrogram of US arrest data
# and print the subtree that a user selects
dnd = as.dendrogram(hclust(dist(USArrests)))
plot(dnd, horiz=TRUE)
dnd2 = identify(dnd)
str(dnd2)
identify.dendrogram = function(dnd) {
#
# Return the dendrogram corresponding to the node a user clicks on.
#
#
# First verify that it is a dendrogram plot corresponding to the
# input dendrogram, and determine if horizontal or veritical
#
n = attributes(dnd)$members
h = attributes(dnd)$height
usr = par()$usr
dx = usr[1] + usr[2]
dy = usr[3] + usr[4]
ok = FALSE
horiz = FALSE
if (abs(n + 1 - dx) < 0.001 && abs((h - dy)/dy) < 0.001) {
ok = TRUE
horiz = FALSE
} else {
if (abs(n + 1 - dy) < 0.001 && abs((h - dx)/dx) < 0.001) {
ok = TRUE
horiz = TRUE
}
}
#
# If the plot matches, call locator() for user input and match the node
#
if (ok) {
crd = locator(1)
if (is.null(crd)) {
return(NULL)
} else {
return(find.node(dnd, 1, crd, horiz))
}
} else {
warning("plot that does not correspond to the dendrogram in the
call.")
return(NULL)
}
}
find.node = function(dnd, offset, crd, horiz) {
#
# find a node in a dendrgram matching the coordinates in crd
# horiz is the plot orientation, see plot(dendrogram)
#
# First see if this node matches the coordinates
#
h = attributes(dnd)$height
n = attributes(dnd)$members
usr = par()$usr
ok.x = FALSE
ok.y = FALSE
if (horiz) {
ok.x = (abs(crd$x - h) / (usr[1] - usr[2])) < 0.05
ok.y = round(crd$y,0) >= offset && round(crd$y,0) <= offset + n
- 1
} else {
ok.y = (abs(crd$y - h) / (usr[4] - usr[3])) < 0.05
ok.x = round(crd$x,0) >= offset && round(crd$x,0) <= offset + n
- 1
}
if (ok.x && ok.y) {
attr = attributes(dnd)
attr$offset = offset
attributes(dnd) = attr
return(dnd)
}
#
# No, so see if there are children of this node that match
#
if (!is.leaf(dnd)) {
nc = length(dnd)
child.offset = offset
for (i in 1:nc) {
#
# Return the match subtree or descend further if no match
#
ret = find.node(dnd[[i]], child.offset, crd, horiz)
if (!is.null(ret)) {
return(ret)
} else {
child.offset = child.offset +
attributes(dnd[[i]])$members
}
}
}
#
# None of the children matched so return NULL
#
return(NULL)
}
David J. States, M.D. Ph.D
University of Texas Health Science Center at Houston
-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David J. States
Sent: Saturday, April 17, 2010 8:35 AM
To: r-help@R-project.org
Subject: [R] Interacting with dendrogram plots, locator() or click()
I would like to explore dendrogam plots interactively. For example, click on a
node and return information about all of the children of that node.
Is there a high level wrapper for locator() or click() that will return the
nearest dendrogram node on a plot?
If not, is there a way to obtain the [x,y] coordinates of all the nodes on a
plot?
Thanks,
David
David J. States, M.D., Ph.D.
Professor of Health Information Science
School of Health Information Sciences
Brown Foundation Institute of Molecular Medicine
University of Texas Health Science Center at Houston
Sarofim Research Building Room 437C
1825 Pressler St.
Houston, TX 77030
Telephone: 713 500 3845
email: david.j.sta...@uth.tmc.edu<mailto:david.j.sta...@uth.tmc.edu>
URL: http://www.stateslab.org
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
