Displaying 20 results from an estimated 4000 matches similar to: "Concatenation and Evaluation"
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.
This e-mail includes an example, and what I think a solution
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
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 can I
get the x-values?
> mydata
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,frame=F,type = "tr"))
but my leaf labels do not fit
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 the ordering is.
In more detail, I am attempting to generate
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 dendrogram using
'as.dendrogram()' from the igraph
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
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 sending
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
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
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 leaves for the first left
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
2012 Feb 23
2
Advice on exploration of sub-clusters in hierarchical dendrogram
Dear R user,
I am a biochemist/bioinformatician, at the moment working on protein
clusterings by conformation similarity.
I only started seriously working with R about a couple of months ago.
I have been able so far to read my way through tutorials and set-up my
hierarchical clusterings. My problem is that I cannot find a way to obtain
information on the rooting of specific nodes, i.e. of
2008 Feb 28
1
Plotting Dendrogram Help Getting Plot to Display Neatly
I have done a cluster analysis doing:
1-clusNorth <-hclust(dist(Artorious)^2, method="ward")
2-clusNorth$labels <-Artorious$Name ## to show the case names and not
numbers
3-dend1 <- as.dendrogram(clusNorth)
4-plot(dend1)
My Dendrogram is now showing the names of my cases in the dataframe on
the x axis
1 OMNICELL INC COM
2 GETTY IMAGES INC
2007 Sep 17
1
side bars on dendrograms with latticeExtra
Dear all,
I am using the heatmap representations of latticeExtra package and I
would be interested to draw color side bars representing the groups of a
factor of interest. From my understanding of :
> help(dendrogramGrob)
...
The 'add' argument can be used for additional annotation at the
base of the dendrogram. It should be a list with one component
for each row,
2009 May 02
1
lattice levelplot axis + custom annotations
How would I set the "scales" property of a lattice levelplot, so that
I can add specific annotations at specific positions?
For example, I have a 200 x 1000 element levelplot. Along the y-axis
(along the 1000-element axis) I would like to add annotations on the
left side of the levelplot at elements 120, 300, 500, and 805, which
represent clusters of interest.
Currently I have
2009 Nov 16
3
Cluster analysis: hclust manipulation possible?
I am doing cluster analysis [hclust(Dist, method="average")] on
data that potentially contains redundant objects. As expected,
the inclusion of redundant objects affects the clustering result,
i.e., the data a1, = a2, = a3, b, c, d, e1, = e2 is likely to
cluster differently from the same data without the redundancy,
i.e., a1, b, c, d, e1. This is apparent when the outcome is
visualized
2008 Aug 01
0
hclust interrogation & use of $merge for dendrogram annotation?
Hi all,
I've been doing some investigation to see if it is possible to implement an hclust/dendrogram related requirement that I've been given. So far ?hclust and a lot of googling haven't provided the information I'm looking for (I've been using R sporadically for a year).
The requirement I have is to:
On a dendrogram plot, draw points at various merge locations, based on
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
2010 Oct 08
2
Heatmap/Color Selection(Key)
Hi
I made heatmap of QTL based on Lod score. Where I have traits in columns and
marker data (rows). I can not cluster both column and rows as I need the
right order for marker data.
Can someone suggest me better way of generating heatmaps especially the
colour key I want to select to visualize the results which are more
interesting to look at.
> library(gplots)
>