Displaying 20 results from an estimated 4000 matches similar to: "font sizes for row.names of dendograms"
2005 Mar 23
1
Complete Linkage Clustering techniques
Dear R
I recently asked for a cluster analysis
Using
* cluster.results <- hclust(iris.dist, method="complete")
* but nothing happened i.e the previous scatterplot matrix still
showed up whereas I was expecting a dendogram.
Could it be that because I had used cutree before on the scatter plots that
it somehow mucked it up. I tried detach then attach and commenced making the
data
2005 May 26
1
Chi Square Test on two groups of variables
Dear R help
I have been trying to conduct a chi square test on two groups of variables
to test whether there is any relationship between the two sets of variables
chisq.test(oxygen, train)
Pearson's Chi-squared test
data: oxygen
X-squared = 26.6576, df = 128, p-value = 1
> chisq.test(oxygen)
Pearson's Chi-squared test
data: oxygen
X-squared = 26.6576, df = 128,
2002 Dec 17
0
Coloured label, terminal branch and bars in dendograms
Dear R-help,
I have performed a hierarchical clustering on some data that I have and
would like to know some nice ways of visualizing it. I have 2 related
questions:
i) How to color the labels AND the terminal branch of a dendogram? This
is my inelegant way of just getting the colored labels.
data(iris) # Formatting data into required format
ir <- iris[ ,-5]
ir.class <- c(
2005 Mar 21
2
Highlighting points in a scatter plot matrix
Dear R
I recently did a scatterplot matrix using the following command
pairs(sleep[c("SlowSleep", "ParaSleep", "logbw", "logbrw", "loglife",
"loggest")],col=1+as.integer(ParaSleep > 5.5 | SlowSleep > 15.7))
this highlighted outlying points for some of the x,y plots that I needed to
identify. Unfortunately this highlights all the x,y
2012 Dec 04
1
How do I get internal nodes of dendograms produced by R?
I am using R for hierarchical clustering of a number of documents.
I have a distance matrix on which I have applied hclust method. When I plot
the result of hclust method, I can see the dendogram plotted. What I need
now is the dendogram stored as a tree in a data structure. My goal is to
automatically label all internal nodes. For that, I need to know, which
leaf nodes make a first level
2004 Jan 04
5
Analyzing dendograms??
I have used heatmap to visualize my microarray data. I have a matrix of
M-values. I do the following.
#The distance between the columns.
sampdist <- dist(t(matrix[,]), method="euclidean")
sclus <- hclust(sampdist, method="average")
#The distance between the rows.
genedist <- dist(matrix[,], method="euclidean")
gclus <- hclust(genedist,
2005 Mar 21
2
NaN
Dear R
What does NaN mean?
I recently did a correlation on a batch of data for some reason it didn't
like one column
cor(sleep,use="complete.obs")
BodyWt BrainWt SlowSleep ParaSleep TotalSleep
BodyWt 1.00000000 0.95584875 -0.3936373 -0.07488845 -0.3428373
BrainWt 0.95584875 1.00000000 -0.3867947 -0.07427740 -0.3370815
SlowSleep -0.39363729
2003 May 06
1
S's plclust and R's hclust
Hello everyone,
Does anyone know how to implement the argument "unit" in R's plclust
function ? I used to use Splus where this argument exists but it has not
been implemented in R's plclust. The reason why I switched from Splus to
R is that Ward's method is not implemented for S's hclust whereas it is
implemented for R's hclust. What I would need is S's plclust
2005 Feb 02
4
(no subject)
can you recommend a good manual for R that starts with a data set and gives
demonstrations on what can be done using R? I downloadedR Langauage
definition and An introduction to R but haven't found them overly useful.
I'd really like to be able to follow some tutorials using a dataset or many
datasets. The datasets I have available on R are
Data sets in package 'datasets':
2005 Feb 28
3
(no subject)
Dear R
Can you tell me how to change the working directory of R
It's just that I have some text files that I wish to save separately from
the R filing structure eg. into C:/my documents and need to change the
working directory of R so that it reads these files . This means if I ever
upgrade the current version of R nothing will be effected.
brett
Brett Stansfield
Environmental Scientist -
2005 May 29
2
joining files after canonical correlation
Dear R,
I recently did a canonical correlation analysis on two subsets of data
(location and weather). So I now have canonical scores for location and
weather. but I'd now like to do a scatterplot matrix using the pairs
statement.
Is there a way to somehow join location.U and weather.V to become a new data
set from which I could undertake a scatterplot matrix of the canonical
variates?
2011 Sep 12
1
hclust and cutree: identifying branches as classes
Good afternoon,
After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches?
This is what we do:
srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward") #creation of hierarchical tree
plclust(srndpchc,hmin=20000) #visualisation
srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes
table(srndpchc20000 )
srndclass20000 =
2004 Jul 02
2
hclust
im using plclust and want the labels to be different colors.
i took a look at getS3method("plot","hclust")
and saw a call to .Internal. i looked at the help on .Internal and dont
know where to go next. any help appreciated!
thanks,
rafael
2005 Feb 02
1
FW: Document1
> -----Original Message-----
> From: Brett Stansfield
> Sent: Wednesday, 19 January 2005 4:25 p.m.
> To: 'S.Ganesh at massey.ac.nz'
> Subject: Document1
>
> <<Doc1.doc>> I was trying to get R to analyse one variable of the file
> Chicken Weight. when I ask
>
> hist(data$weight)
> R says "x must be numeric"
> yet when I
2005 Mar 16
2
(no subject)
Dear R
I'm trying to do a correlation matrix for some variables I have.
Unfortunately there are some NA entries for some of the variables
I tried the following
cor(sleep[c("logbw", "logbrw", "SlowSleep", "ParaSleep", "loglife",
"loggest")])
but it told me
Error in cor(sleep[c("logbw", "logbrw",
2005 May 31
1
Loading matrices and other things
Hi all,
I'm new to R, so needless to say I have a couple questions (which I hope
I haven't missed through the documentation).
I have several files in lower triangular matrix form. For each of these
matrices, I want to perform some form of hierarchical clustering on each
matrix and capture the output of the clustering.
The first problem I run into is actually loading the matrix file
2004 Sep 10
1
swiss.x
Is the swiss data set in R the same as S dataset swiss.x .
I was trying out some clustering by doing the following that I got from
Venables and Ripley's book.
h<-hclus(dist(swiss.x), method= "connected")
plclust(h)
cutree(h,3)
plclust(clorder(h,cutree(h,3)))
I tried swiss instead of swiss.x, it doesnot seem happy.
Thanks ../Murli
2017 Jun 21
1
getting error while trying to make dendogram based on gene expression
I am trying to make dendogram based on gene expression matrix , but getting
some error:
I
countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F)
colnames(countMatrix)
count_matrix <- countMatrix[,-1] # remove first column
(gene names)
rownames(count_matrix) <- countMatrix[,1] #added first column gene
names as rownames)
>
2005 Mar 27
1
Subject [applying labels to a scatter plot matrix]
Dear R
Is there a way to apply row names as labels to a scatter plot matrix ,
I tried
pairs(dogs, labels=row.names)
Error in strwidth(labels, "user") : cannot coerce type closure to character
vector
I'm not sure what this means, however maybe you might know of a way to do
this?
brett stansfield
2000 Aug 31
2
Multiv / hierclust / plclust
I use hierclust (hierarchical clustering) in multiv package. In the
documentation it is said that plclust (plotting a dendrogram) is
available in S-plus. Can I find it anywhere (I have searched through
http://lib.stat.cmu.edu/S and found only quotations of plclust in
multiv) or is it only part of the S package (which I don't have)?
Thanks
---------------
Charles RAUX,
Laboratoire