Displaying 8 results from an estimated 8 matches for "dend2".
Did you mean:
dendf
2005 Jul 11
1
indexing into and modifying dendrograms
...ly rather associate with the node than the edge
## but current plotting function has no notion of nodetext
addE <- function(n) {
if(!is.leaf(n)) {
attr(n, "edgePar") <- list(p.col="plum")
attr(n, "edgetext") <- attr(n,"cNum")
}
n
}
dend2 <- dendrapply(dend1, addE)
## overlays the cNum ("cluster number") attribute on dendrogram
plot(dend2, main = "dend2")
## why does no plum polygon appear around the '4' for the root
## edge?
## swap order of clusters 2 and 3,
## i.e. 'flip' cluster 4
dend3 &l...
2007 Jun 13
2
Formatted Data File Question for Clustering -Quickie Project
...quot;triangle" type and show inner nodes:
plot(dend1, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),
type = "t", center=TRUE)
plot(dend1, edgePar=list(col = 1:2, lty = 2:3), dLeaf=1, edge.root =
TRUE)
plot(dend1, nodePar=list(pch = 2:1,cex=.4*2:1, col = 2:3), horiz=TRUE)
dend2 <- cut(dend1, h=70)
plot(dend2$upper)
## leafs are wrong horizontally:
plot(dend2$upper, nodePar=list(pch = c(1,7), col = 2:1))
## dend2$lower is *NOT* a dendrogram, but a list of .. :
plot(dend2$lower[[3]], nodePar=list(col=4), horiz = TRUE, type = "tr")
## "inner" and &quo...
2011 Jan 25
1
dendrogram plot does not draw long labels ?
Hello,
It seems that the plot function for dendrograms does not draw labels when
they are too long.
> hc <- hclust(dist(USArrests), "ave")
> dend1 <- as.dendrogram(hc)
> dend2 <- cut(dend1, h=70)
> dd <- dend2$lower[[1]]
> plot(dd) # first label is drawn
> attr(dd[[1]], "label") <- "aaaaaaaaaaaaaaaaaa"
> plot(dd) # first label is NOT drawn
Is this expected ?
Is it possible to force the drawing ?
Thank you,
Karl
[[alternative...
2007 Oct 26
2
cut.dendrogram and cutree
Hi!
In the example:
hc <- hclust(dist(USArrests), "ave")
dend1 <- as.dendrogram(hc)
dend2 <- cut(dend1, h=70)
Do the branches "Branch 1", "Branch 2", "Branch 2"...in dend2$upper
str(dend2$upper)
--[dendrogram w/ 2 branches and 4 members at h = 152]
|--[dendrogram w/ 2 branches and 2 members at h = 77.6]
| |--leaf "Branch 1" (h= 38.5...
2002 Mar 05
1
no labels when plotting dendrograms
...39;t figure out how to add labels to the nodes.
For example, this example from the dendrogram documentation
plots a dendrogram without labels:
library(mva)
data(USArrests)
hc <- hclust(dist(USArrests), "ave")
str(dend1 <- as.dendrogram(hc))
plot(dend1)
dend2 <- cut(dend1, h=70)
plot(dend2$upper)
plot(dend2$lower[[3]])
So... does anyone know how to cut an hclust object and get a
list of hclust objects, or how to plot a dendrogram object with
labels? Thanks.
David Marimont
NXP Data Analysis, Inc.
http://www.nxpdata.com
-.-.-.-....
2016 Apr 17
0
use hjust or vjust with dendextend
Following "Introduction to dendextend" from Tal Galili, I applied this
code on iris data:
##
library(dendextend)
library(dendextendRcpp)
library(ggplot2)
dend2 <- iris[1:30,-5] %>% dist %>% hclust %>% as.dendrogram %>%
set("branches_k_color", k=3) %>% set("branches_lwd", rep(1,4)) %>%
set("branches_lty", rep(1,6)) %>% set("labels_colors") %>%
set("labels_cex", c(1.0,1.0)) %>...
2012 May 24
4
Manually modifying an hclust dendrogram to remove singletons
Dear R-Help,
I have a clustering problem with hclust that I hope someone can help
me with. Consider the classic hclust example:
hc <- hclust(dist(USArrests), "ave")
plot(hc)
I would like to cut the tree up in such a way so as to avoid small
clusters, so that we get a minimum number of items in each cluster,
and therefore avoid singletons. e.g. in this example, you can see
2013 May 01
1
help understanding hierarchical clustering
...t,"average")
print(clusa)
Call:
hclust(d = distmat, method = "average")
Cluster method : average
Distance : bray
Number of objects: 8036
print(dend1 <- as.dendrogram(clusa))
'dendrogram' with 2 branches and 8036 members total, at height 0.3194225
dend2 <- cut(dend1, h=0.07)
a complete run with plots is available here :
http://nbviewer.ipython.org/5492912
i'm trying try to group together the species (idcode's) that are sharing similar environmental parameters
like (looking at the plots) i should be able to retrieve the list of id...