Dear R Community,
Is there a way to adjust the line width of the dendrogram in heat map.2
function? I tried "lwd", but it didn't work...
Also, is there a way to adjust the general height/width/position of the
dendrogram using heatmap.2 function? I feel the portion of the dendrogram is
huge compa
Hello everyone,
I have generated a dendrogram by applying a hierarchical clustering
technique to a graph. Given this dendrogram I am trying to efficiently
find/ map/ label the dendrogram branches to their corresponding graph
edges. Using dendextend I am able to partition the leaves, obtain
subgrap
Hi.
I have two question!
1) Is there any way to draw a dendrogram for k-modes?
I used klaR pacakges for kmodes analysis to deal with categorical variables.
i heard about the "Clustergram"
Url = {http://www.schonlau.net/clustergram.html}
but i only found the example of Clustergram for K-m
Le mercredi 16 janvier 2013 à 07:29 +0200, Ibrahim Sobh a écrit :
> Dear I am using the 'as.dendrogram' function from the 'stats' library
> to convert from an hclust object to a dendrogram with a dataset of
> size
> ~3 (an example code is below). I need the dendrogram structure to
> use the
Dear I am using the 'as.dendrogram' function from the 'stats' library to
convert from an hclust object to a dendrogram with a dataset of size
~3 (an example code is below). I need the dendrogram structure to
use the "dendrapply" and "attributes" functions and to access the child
nodes, I
Hi Elyakhlifi,
You can try this:
hc <- hclust(dist(USArrests), "ave")
plot(hc, cex = .5)
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Heb
Hello.
I have a small problem when I want to display a dendrogram for about 450
varieties.
The label of theses varieties is too big and we can not see thems well.
How can I do to resize the label smaller?
Can you help me please?
Thanks.
[[alternative HTML version deleted]]
_
Dear users,
I am trying to extract the fusion levels from a dendrogram (in my case,
phylogenetic trees in the 'phylo' format of APE). So far, I have not been
successful. I can't believe there is not a library to do it, but I can't find a
function that would extract the fusion levels.
Do you kn
Besides the facility to plot dendrograms vertically and
horizontally, is there any chance to plot them mirrored, i.e.,
instead of shaping them like ,-, and E have them like '-' and 3
(I hope that my minimalistic visualization is legible)?
If there is, how might that be accomplished (other than mir
I have tried to use rect.hclust() to draw a rectangle around a set of
leaves, but am running into trouble.
The rect.hclust() is drawing two rects instead of one, and of the
wrong size:
scoreClusterObj <- hclust(scoreDistanceObj, method=clustMethod)
order <- scoreCluster
> "MK" == Marcin Kozak
> on Sat, 17 Jan 2009 10:14:10 +0100 writes:
MK> Hi, I am clustering objects using the agnes() function
MK> and the UPGMA clustering method (function =
MK> "average"). Everything works well, but apparently
MK> something is wrong with the dendrogr
Hi,
I am clustering objects using the agnes() function and the UPGMA
clustering method (function = "average"). Everything works well, but
apparently something is wrong with the dendrogram. For example:
x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3)
y<-c(110,111,110.2,112.1,119.5,122.
Take a look at the las() function o ?par. It permits you to choice
labels directions.
__
Rodrigo Aluizio
Em 21/11/2008, às 17:14, "Richardson, Patrick" <[EMAIL PROTECTED]
g> escreveu:
!#x000a
Is there any way to change the orientation of the labels on the end
of the dendrograms
[mailto:[EMAIL PROTECTED]
Sent: Friday, November 21, 2008 2:28 PM
To: Richardson, Patrick
Cc: 'r-help@r-project.org'
Subject: Re: [R] Dendrogram labels
Try:
b<-as.dendrogram(a); plot(b, horiz=TRUE).
that should help.
fan
On Nov 21, 2008, at 2:14 PM, Richardson, Patrick wrote:
Is
ional Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
-Original Message-
From: Fan Yang [mailto:[EMAIL PROTECTED]
Sent: Friday, November 21, 2008 2:28 PM
To: Richardson, Patrick
Cc: 'r-help@r-project.org'
Subject: Re:
Is there any way to change the orientation of the labels on the end of the
dendrograms to horizontal rather than vertical? If so, how can I do that.
Below is my code, but I'm not sure which argument(s) I can use to change the
label(s) (if it is possible to do).
a <- hclust(z, method = "comple
Is there any way to change the orientation of the labels on the end of the
dendrograms to horizontal rather than vertical? If so, how can I do that.
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute
Alex
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Alex Reynolds
> Sent: Wednesday, 7 May 2008 12:26 a.m.
> To: r-help@r-project.org
> Subject: [R] Dendrogram label size
>
> Is it possible to resize the labels
Is it possible to resize the labels in a dendrogram without applying
circles and triangles to edges?
I tried cex.labels:
plot(scoreDendogramObj, horiz=TRUE, axes=FALSE, cex.labels=0.8)
but that didn't have any effect.
Thanks,
Alex
__
R-help@r-pro
Try:
plot(as.dendrogram(dd1), horiz = TRUE, nodePar = list(lab.cex = .4))
On Thu, Mar 27, 2008 at 1:08 PM, Lassana TOURE <[EMAIL PROTECTED]> wrote:
> I am using the two functions hclust and plot to draw a dendrogram. The
> result is a vertical dendrogram , but I prefer a horizontal one.
>
> Need
Lassana TOURE wrote:
> I am using the two functions hclust and plot to draw a dendrogram. The
> result is a vertical dendrogram , but I prefer a horizontal one.
>
> Need help.
Take a look at `?dendrogram'.
HTH,
Henric
>
> This is my script:
>
>
>
> dd1=hclust(d1, method="ward")
>
> pl
I am using the two functions hclust and plot to draw a dendrogram. The
result is a vertical dendrogram , but I prefer a horizontal one.
Need help.
This is my script:
dd1=hclust(d1, method="ward")
plot(dd1)
[[alternative HTML version deleted]]
__
ří Voller <[EMAIL PROTECTED]>
To: r-help@r-project.org
Sent: Sun, 23 Mar 2008 22:48:33 +0800 (SGT)
Subject: [R] Exporting of R dendrogram object in the format of Eisen´s Cluster
Dear R-users,
I would like to use Cluster 3.0 for my data because of its zooming, link out
and copy (gene)labels
Dear R-users,
I would like to use Cluster 3.0 for my data because of its zooming, link out
and copy (gene)labels into clipboard options. Unfortunately the program
doesnt allow use of the distance metrics I would like to use. I would like
to ask if there is some library, that allows saving dendrog
Thank you for your reply Wolfgang
I've seen these examples but my problem is that I don't know how to
make the input data out of my given data. According to the example
below hclust is making the clustering and will result in hclust object
hc. In my case the clustering is already done and I need to
Hi Risto,
You could try
example("dendrogram")
best wishes
Wolfgang
noorpiilur scripsit:
> Hey group,
>
> I have a problem of drawing dendrogram as the result of my program
> written in C. My algorithm is a approximation algorithm for single
> linkage method. AS a result I will get th
Hey group,
I have a problem of drawing dendrogram as the result of my program
written in C. My algorithm is a approximation algorithm for single
linkage method. AS a result I will get the following data:
[Average distance] [cluster A] [cluster B]
For example:
42.593141 1 26
42.593141
Hi!
To label your dendrogram edges with the path to each of them, execute the
following script (assuming that your dendrogram is 'dend', see last 2
lines).
dendrapplyGlobal <- function(dend,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attr
assign then names to the rows in the dataframe:
row.names(d) <- c("Italy", "France", "Spain", ...)
On 10/14/07, Alessandra Trimarchi <[EMAIL PROTECTED]> wrote:
> Dear r-help mailing list,
> here there is a data-frame of 24 observations and 7 variables.
>W3 D3P3 T3 U3 V3 R3
> 1 31.3
Dear r-help mailing list,
here there is a data-frame of 24 observations and 7 variables.
W3 D3P3 T3 U3 V3 R3
1 31.3 52 50200 1.67 59.4 55 57
2 33.0 61 45684 0.83 62.0 64 85
3 29.6 55 30455 0.60 56.6 45 52
4 28.0 59 8858 0.96 22.1 40 45
5 29.1 53 8334 0.63 42.9 46 51
6 23.1 79
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