Hi All: I am clustering 500 genes using hclust of R. Visualizing cluster membership becomes difficult with so many genes in each cluster...Is there a way of printing the dendrogram in multiple pages so that I can clearly see what is in each cluster? Thanks in advance. Karthi.
>>>>> "KarthiS" == Subramanian Karthikeyan <Subramanian_Karthikeyan at hc-sc.gc.ca> >>>>> on Wed, 24 Sep 2003 13:04:04 -0400 writes:KarthiS> Hi All: I am clustering 500 genes using hclust of KarthiS> R. Visualizing cluster membership becomes KarthiS> difficult with so many genes in each cluster...Is KarthiS> there a way of printing the dendrogram in multiple KarthiS> pages so that I can clearly see what is in each KarthiS> cluster? - Use dd <- as.dendrogram(hc) on your hclust result `hc', then dd[1] gives the first branch, dd[1][2] the 2nd sub-branch of the first branch, etc., see the examples on ?dendrogram. - The package "maptree" has also tools for this, particularly prune.clust() KarthiS> Thanks in advance. you're welcome. -- Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1228 <><
Thanks Martin,
Cutting the dendrogram as you suggested solved the problem. I have
another question along the same lines... If samples x1, x2, y4,y5, z6 are
clustered together, is there a way of extracting this information (i.e.
name of the samples clustered together) and saving it in a file?
Thanks again,
Karthi.
Martin Maechler
<maechler at stat.ma To: "Subramanian
Karthikeyan" <Subramanian_Karthikeyan at hc-sc.gc.ca>
th.ethz.ch> cc: r-help at
stat.math.ethz.ch
Subject: Re: [R] splitting
clusters
2003-09-25 03:56
AM
Please respond to
Martin Maechler
>>>>> "KarthiS" == Subramanian Karthikeyan
<Subramanian_Karthikeyan at hc-sc.gc.ca>>>>>> on Wed, 24 Sep 2003 13:04:04 -0400 writes:
KarthiS> Hi All: I am clustering 500 genes using hclust of
KarthiS> R. Visualizing cluster membership becomes
KarthiS> difficult with so many genes in each cluster...Is
KarthiS> there a way of printing the dendrogram in multiple
KarthiS> pages so that I can clearly see what is in each
KarthiS> cluster?
- Use dd <- as.dendrogram(hc) on your hclust result `hc',
then dd[1] gives the first branch, dd[1][2] the 2nd sub-branch of
the first branch, etc., see the examples on
?dendrogram.
- The package "maptree" has also tools for this,
particularly prune.clust()
KarthiS> Thanks in advance.
you're welcome.
--
Martin Maechler <maechler at stat.math.ethz.ch>
http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
I am really wondering if there is a way of exporting the names of the
samples/variables clustered within a dendrogram object into a TEXT file.
Any ideas?
Thanks,
Karthi.
"Liaw, Andy"
<andy_liaw at merck. To:
"'Subramanian Karthikeyan'" <Subramanian_Karthikeyan at
hc-sc.gc.ca>
com> cc:
Subject: RE: [R] splitting
clusters
2003-09-25 03:10
PM
As Robert Gentleman pointed out to you on the BioC list, cutree() gives you
the cluster membership.
Andy
> -----Original Message-----
> From: Subramanian Karthikeyan
> [mailto:Subramanian_Karthikeyan at hc-sc.gc.ca]
> Sent: Thursday, September 25, 2003 1:10 PM
> To: Martin Maechler; r-help at stat.math.ethz.ch
> Subject: Re: [R] splitting clusters
>
>
>
> Thanks Martin,
>
> Cutting the dendrogram as you suggested solved the problem. I have
> another question along the same lines... If samples x1, x2,
> y4,y5, z6 are clustered together, is there a way of
> extracting this information (i.e. name of the samples
> clustered together) and saving it in a file?
>
> Thanks again,
> Karthi.
>
>
>
>
>
>
>
>
>
> Martin Maechler
>
>
> <maechler at stat.ma To:
> "Subramanian Karthikeyan"
> <Subramanian_Karthikeyan at hc-sc.gc.ca>
> th.ethz.ch> cc:
> r-help at stat.math.ethz.ch
>
> Subject: Re:
> [R] splitting clusters
>
> 2003-09-25 03:56
>
>
> AM
>
>
> Please respond to
>
>
> Martin Maechler
>
>
>
>
>
>
>
>
>
>
>
>
> >>>>> "KarthiS" == Subramanian Karthikeyan
> <Subramanian_Karthikeyan at hc-sc.gc.ca>
> >>>>> on Wed, 24 Sep 2003 13:04:04 -0400 writes:
>
> KarthiS> Hi All: I am clustering 500 genes using hclust of
> KarthiS> R. Visualizing cluster membership becomes
> KarthiS> difficult with so many genes in each cluster...Is
> KarthiS> there a way of printing the dendrogram in multiple
> KarthiS> pages so that I can clearly see what is in each
> KarthiS> cluster?
>
> - Use dd <- as.dendrogram(hc) on your hclust result `hc',
> then dd[1] gives the first branch, dd[1][2] the 2nd sub-branch of
> the first branch, etc., see the examples on
> ?dendrogram.
>
> - The package "maptree" has also tools for this,
> particularly prune.clust()
>
> KarthiS> Thanks in advance.
>
> you're welcome.
> --
> Martin Maechler <maechler at stat.math.ethz.ch>
> http://stat.ethz.ch/~maechler/
> Seminar fuer Statistik,
> ETH-Zentrum LEO C16 Leonhardstr. 27
> ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
> phone: x-41-1-632-3408 fax: ...-1228 <><
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
>
Hello Does anyone know how to truncate and axis in R? Thanks Diego -- _______________________________________ Diego Mauricio Riano Pachon Biologist Institute of Biology and Biochemistry Potsdam University Karl-Liebknecht-Str. 24-25 Haus 20 14476 Golm Germany Tel:0331/977-2809 http://bioinf.ibun.unal.edu.co/~gotem http://www.geocities.com/dmrp.geo/
Diego Riano wrote:> Hello > > Does anyone know how to truncate and axis in R? >Not sure what you mean, but do to plot arguments xlim and ylim do what you want? See help(par) for these and other plot controls. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 jasont at indigoindustrial.co.nz