Displaying 20 results from an estimated 27 matches for "dend".
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2015 May 18
2
A "bug" in plot.dendrogram - can't plot lty with character color
The problem:
===========
Once a dendrogram has a branch with both a line type AND a color (which is
a character color), the plot.dendrogram function will not plot and return
an error.
I say this is a bug because (I believe), we would like a dendrogram to be
able to use character colors, while also allowing control over line types....
2007 Nov 25
2
accessing the "address" of items in a recursive list
Dear useRs,
I am working on a project involving the clustering of a large dataset. I need to extract specific sub-clusters from the parent dendrogram for further analysis. The data is too large for the use of convenient tools such as identify.clust (it selects the specific group of interest on a graph), so alternatively I have saved the plot as a large image file so that it can be printed or viewed piecemeal. My problem is this: when I f...
2015 May 20
0
Probably a "bug" in the dendextend package
>>>>> Tal Galili <tal.galili at gmail.com>
>>>>> on Mon, 18 May 2015 23:01:44 +0300 writes:
> The problem:
> ===========
> Once a dendrogram has a branch with both a line type AND a color (which is
> a character color), the plot.dendrogram function will not plot and return
> an error.
If the dendrogram has been messed up ... see below.
> I say this is a bug because (I believe), we would like a dendrogram t...
2005 May 18
0
dendrogram and dendrapply
Hi all,
I think I have some problems to use correctly the function dendrapply.
Let suppose dend is a dendrogram object.
I would likde to know the cardinal number of leaves depending of each
node of the tree dend.
It is right that the command attr(dend,"members") gives the total number
of leaves, and
attr(dend[[1]],"members") gives the number of le...
2008 Feb 04
1
Concatenation and Evaluation
...sn't work. So I apologize in advance
if this is painfully obvious, but I've run out of ideas and would
really appreciate any input.
My situation is this, I'm importing a number of tab delimited text
files that contain chromatogram data that I am trying to display
adjacent to a dendrogram. Since I look at multiple files I import
them as file1, file2, file3, etc. To display them in the order that
comes from the dendrogram I want to use order.dendrogram, which gives
me a vector of numbers that is the order which I want the
chomatograms to be displayed.
Here's the...
2004 May 06
1
question about plot.dendrogram
hi all,
i'm trying to plot a dendrogram with labeled leaves
>rownames(f)<-v.names
>v<-rowMeans(f, na.rm=T)
>clust<-hclust(dist(v))
>dend<-as.dendrogram(clust,hang=0.05)
>clust2<-cut(dend, h=0.5)
>class(clust2$low[[1]])
>[1] "dendrogram"
then
>plot(clust2$low[[1]],horiz=TRUE,fram...
2005 Nov 02
1
x/y coordinates of dendrogram branches
Dear R-users,
I need some help concerning the plotting of dendrograms for hierarchical
agglomerative clustering.
The agglomeration niveau of each step should be displayed at the
branches of the dendrogram.
For this I need the x/y coordinates of the branch-agglomerations of the
dendrogram.
The y-values are known (the heights of the agglomeration), but how ca...
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
I am having trouble displaying a dendrogram of evolutionary
relationships (a phylogram imported from the ape package) as the
vertical component of a heatmap, but keeping the hierarchical
clustering of the horizontal component. The relationships of the
vertical component in the generated heatmap are not that of the
dendrogram, although...
2000 Jan 17
1
lwd patches for "contour"
...;identify", do_identify, 0, 11, 6, PP_FUNCALL},
{"strheight", do_strheight, 0, 11, 3, PP_FUNCALL},
{"strwidth", do_strwidth, 0, 11, 3, PP_FUNCALL},
! {"contour", do_contour, 0, 11, 6, PP_FUNCALL},
{"image", do_image, 0, 11, 5, PP_FUNCALL},
{"dend", do_dend, 0, 111, 6, PP_FUNCALL},
{"dend.window", do_dendwindow, 0, 111, 6, PP_FUNCALL},
--- 644,650 ----
{"identify", do_identify, 0, 11, 6, PP_FUNCALL},
{"strheight", do_strheight, 0, 11, 3, PP_FUNCALL},
{"strwidth", do_strwidth, 0, 11, 3, PP_...
2004 Jul 02
2
hclust
im using plclust and want the labels to be different colors.
i took a look at getS3method("plot","hclust")
and saw a call to .Internal. i looked at the help on .Internal and dont
know where to go next. any help appreciated!
thanks,
rafael
2011 Apr 11
1
heatmap clustering dendrogram export
Hi,
I am a beginner for R.
I had use gplots to generate a heatmap as following:
>heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE,
trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2,
cexCol=0.6)
It work well. It generate heatmap whith rcolumn clustering dendrogram and I
can export a very nice graph. But I don not know how to export the column
clusteri...
2008 Jan 08
0
Status of Timezone support / Handeling DTSTART; TZID="(GMT-05.00) Eastern Time (US & Canada)":20080107T123000
I can not tell from the docs or from the mailing list what is the
state of timezone support in the iCalendar package?
If I want to parse an iCalendar file that has non utc dstarts and
dends will it convert those times to UTC or otherwise allow me to do
that?
When I tried to parse an iCalendar input file started off with
something like this:
BEGIN:VCALENDAR
METHOD:REQUEST
PRODID:Microsoft CDO for Microsoft Exchange
VERSION:2.0
BEGIN:VTIMEZONE
TZID:(GMT-05.00) Eastern Time (US &a...
2010 Apr 09
3
Problems with Fax over TDM410P
...g=fxs_ks
group=0
channel => 3
context=inside
faxdetect=incoming
immediate=no
signalling=fxo_ks
group=1
channel => 4
What should we do in order to make it work ok? we really need to put this
working, i've heard that asterisk does not work very well with fax, but at
least it should try to dend it, not to get frozen :S
Thanks in advance for all your help!
Regards
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2005 May 28
1
Forcing ticks in plot for hclust object outside the limits
Hello!
I have the following problem.
I would like to plot the hclust object "hcd" (bellow, at the end of the
mail) with ticks at seq(0.05,0.25,by=0.05). I tried using the code
plot(hcd)
and
plot(hcd,axes=FALSE)
axis(2,seq(0.05,0.25,by=0.05))
In both cases, the resoult is the same, ticks at 0.05 and 0.25 are not
printed. I tried changing the ylim argumet in plot, however I got a
2010 Jun 17
1
plotting radial dendrograms
Dear list,
I am trying to plot a radial dendrogram using the ape package, which
requires my data to be of class 'phylo'. Currently I have my
dendrogram stored as an object of class 'dendrogram' which was
produced from an outside bit of C code, but was made into an object of
class 'igraph.eigenc' and converted to a dend...
2003 Jul 17
2
i need help in cluster analyse
Hello,
My name is Rodrigo, I am using R program and I have a trouble.
I am trying to do a dendrogram with genetics information.
Let me explain...
The Similarity Matrix was already did, and with this matrix I want to construct a dendrogram.
So, the distance is done. I need to transform this matrix (that I have) in a dendrogram,
I woud be very grateful if someone could help me.
PS: I am send...
2005 Oct 23
1
Coloring leaves, twigs and labels in plot.dendrogram()
Core developers,
I couldn't find any simple way to send a vector of colors to apply to each
terminal in plot.dendrogram() or plot.hclust()---I asked R-help about it a
few weeks ago and didn't get any response---so I hacked that functionality
into the plot.dendrgram code (see below for hacked function plus
examples)....
Is there any chance this functionality could be added to the base code?
Unquestio...
2005 Jul 06
1
Help: Mahalanobis distances between 'Species' from iris
...from 'irisSAS' data?
D = matrix(0, n, n)
nam = c('Set', 'Ver', 'Vir')
rownames(D) = nam
colnames(D) = nam
k = 0
for (i in 1:n) {
for (j in 1:i) {
k = k+1
D[i,j] = Mah[k]
D[j,i] = Mah[k]
}
}
D=sqrt(D) #D2 -> D
library(mclust)
dendroS = hclust(as.dist(D), method='single')
dendroC = hclust(as.dist(D), method='complete')
win.graph(w = 3.5, h = 6)
split.screen(c(2, 1))
screen(1)
plot(dendroS, main='Single', sub='', xlab='', ylab='', col='blue')
screen(2)
plot(dendroC, mai...
2023 Mar 23
1
`dendrapply` Enhancements
Hello Aidan,
Sorry for dropping this for a while.
? Thu, 2 Mar 2023 21:03:59 +0000
"Lakshman, Aidan H" <AHL27 at pitt.edu> ?????:
> //after
> curnode = eval(lang3(R_Bracket2Symbol, parent->node, DEND_IND), env);
lang3() always constructs a new language object. If you do end up using
eval(), it may make sense to move lang3() out of the loop and reuse the
existing object by referring to the DEND_IND variable using its symbol,
like it's done in the lapply() implementation.
> The problem i...
2023 Feb 23
1
`dendrapply` Enhancements
Hi everyone,
My apologies if this isn?t the right place to submit this?I?m new to the R-devel community and still figuring out what is where.
If people want to skip my writeup and just look at the code, I?ve made a repository for it here: https://github.com/ahl27/new_dendrapply/tree/master. I?m not quite sure how to integrate it into a fork of R-devel; the package structure is different from what I?m used to.
I had written a slightly improved version of dendrapply for one of my research projects, and my advisor encouraged me to submit it to the R project. It took m...