Question: heatmap genenames
0
14.6 years ago by
Claire Wilson280
Claire Wilson280 wrote:
Dear all, I have been using the heatmap function to visualise my data and would like to obtain a list of my genes in the same order that they appear in the heatmap. I have looked through the mail archives and tried just creating a dendogram and using order.dendogram but have so far been unsuccessful. Can anyone point me in the right direction? cheers claire -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
• 530 views
modified 14.5 years ago by Francois Pepin1.3k • written 14.6 years ago by Claire Wilson280
0
14.6 years ago by
michael watson IAH-C3.4k wrote:
Hi Claire What does your call to heatmap look like? Do you cluster using something like hclust() first, or do you just put in a call to heatmap? Mick -----Original Message----- From: Claire Wilson [mailto:ClaireWilson@picr.man.ac.uk] Sent: Thu 11/4/2004 2:06 PM To: BioC mailing list Cc: Subject: [BioC] heatmap genenames Dear all, I have been using the heatmap function to visualise my data and would like to obtain a list of my genes in the same order that they appear in the heatmap. I have looked through the mail archives and tried just creating a dendogram and using order.dendogram but have so far been unsuccessful. Can anyone point me in the right direction? cheers claire -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}} _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
0
14.6 years ago by
Claire Wilson280
Claire Wilson280 wrote:
Hello, Many thanks for your reply, I have tried repeating the clustering done by heatmap using hclust to obtain the row order as follows: d <- dist(mydata) hc.d <- hclust(d) gene.order <- hc.d$order and compared the order to what I see on a heatmap when I do heatmap(mydata) However, it would appear that the ordering of genes within a heatmap made from heatmap(mydata) is different to that seen if a dendrogram is made from from hc.d. So I am thinking something else happens after doing the hierarchical clustering within the heatmap function, but I have so far been unsuccessful in my attempts to try and work out what it is. Claire > Dear Claire, > > if I remember well heatmap uses hclust as default clustering > function with > distances given by "dist" that, in turn, uses "euclidean" > distance as default. > > So, I guess that you should be able to obtain the desired > order easily runing > > hclust(dist( your.data ))$order > > or something like > > my.cluster<-hclust(dist( my.data )) > rownames( my.data )[my.cluster$order] > > > Let me know if it works > Alessandro > > > At 15.06 04/11/2004, you wrote: > >Dear all, > > > >I have been using the heatmap function to visualise my data and would > >like to obtain a list of my genes in the same order that > they appear in > >the heatmap. I have looked through the mail archives and tried just > >creating a dendogram and using order.dendogram but have so far been > >unsuccessful. Can anyone point me in the right direction? > > > >cheers > > > >claire > > > >-------------------------------------------------------- > > > > > >This email is confidential and intended solely for the use > o...{{dropped}} > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}} ADD COMMENTlink written 14.6 years ago by Claire Wilson280 If I remember correctly, heatmap does reorder the genes with respect to the dendrogram (not with R right now). Try using heatmap( ....., rowV=1:n) where n is the number of genes. Also, check the capitalization for rowV. Sean On Nov 4, 2004, at 12:03 PM, Claire Wilson wrote: > > Hello, > > Many thanks for your reply, I have tried repeating the clustering done > by heatmap using hclust to obtain the row order as follows: > > d <- dist(mydata) > hc.d <- hclust(d) > gene.order <- hc.d$order > > and compared the order to what I see on a heatmap when I do > > heatmap(mydata) > > However, it would appear that the ordering of genes within a heatmap > made from heatmap(mydata) is different to that seen if a dendrogram is > made from from hc.d. So I am thinking something else happens after > doing > the hierarchical clustering within the heatmap function, but I have so > far been unsuccessful in my attempts to try and work out what it is. > > Claire > > >> Dear Claire, >> >> if I remember well heatmap uses hclust as default clustering >> function with >> distances given by "dist" that, in turn, uses "euclidean" >> distance as default. >> >> So, I guess that you should be able to obtain the desired >> order easily runing >> >> hclust(dist( your.data ))$order >> >> or something like >> >> my.cluster<-hclust(dist( my.data )) >> rownames( my.data )[my.cluster$order] >> >> >> Let me know if it works >> Alessandro >> >> >> At 15.06 04/11/2004, you wrote: >>> Dear all, >>> >>> I have been using the heatmap function to visualise my data and would >>> like to obtain a list of my genes in the same order that >> they appear in >>> the heatmap. I have looked through the mail archives and tried just >>> creating a dendogram and using order.dendogram but have so far been >>> unsuccessful. Can anyone point me in the right direction? >>> >>> cheers >>> >>> claire >>> >>> -------------------------------------------------------- >>> >>> >>> This email is confidential and intended solely for the use >> o...{{dropped}} >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use...{{dropped}}
0
14.6 years ago by
Switzerland
Martin Maechler330 wrote:
>>>>> "Claire" == Claire Wilson <clairewilson@picr.man.ac.uk> >>>>> on Thu, 4 Nov 2004 14:06:28 -0000 writes: Claire> I have been using the heatmap function to visualise Claire> my data and would like to obtain a list of my genes Claire> in the same order that they appear in the heatmap. I Claire> have looked through the mail archives and tried just Claire> creating a dendogram and using order.dendogram but Claire> have so far been unsuccessful. Can anyone point me Claire> in the right direction? Right directions: 1) Please do read the posting guide (for R-help) that applies here as well: ---> http://www.R-project.org/posting-guide.html 2) The posting guide tells among other things, to really read the help page of function. ?heatmap and look at the section called "Value:" ==> I'm pretty sure that r <- heatmap(...........) r$colInd ## gives you the desired ordering. Regards, Martin Maechler, ETH Zurich ADD COMMENTlink written 14.6 years ago by Martin Maechler330 Answer: heatmap genenames 0 14.6 years ago by michael watson IAH-C3.4k wrote: Hi Claire I will have a look at this tomorrow when I have R actually in front of me, but in the meantime, may I reccomend that you specifically use hclust and dist when using heatmap? I always do - it gives you more control over what exactly is going on! So do: d <- dist(mydata) hc <- hclust(d) heatmap(mydata, RowV=as.dendrogram(hc)) gene.order = hc$order Mick -----Original Message----- From: Claire Wilson [mailto:ClaireWilson@picr.man.ac.uk] Sent: Thu 11/4/2004 5:03 PM To: alessandro ambrosi Cc: BioC mailing list Subject: RE: [BioC] heatmap genenames Hello, Many thanks for your reply, I have tried repeating the clustering done by heatmap using hclust to obtain the row order as follows: d <- dist(mydata) hc.d <- hclust(d) gene.order <- hc.d$order and compared the order to what I see on a heatmap when I do heatmap(mydata) However, it would appear that the ordering of genes within a heatmap made from heatmap(mydata) is different to that seen if a dendrogram is made from from hc.d. So I am thinking something else happens after doing the hierarchical clustering within the heatmap function, but I have so far been unsuccessful in my attempts to try and work out what it is. Claire > Dear Claire, > > if I remember well heatmap uses hclust as default clustering > function with > distances given by "dist" that, in turn, uses "euclidean" > distance as default. > > So, I guess that you should be able to obtain the desired > order easily runing > > hclust(dist( your.data ))$order > > or something like > > my.cluster<-hclust(dist( my.data )) > rownames( my.data )[my.cluster\$order] > > > Let me know if it works > Alessandro > > > At 15.06 04/11/2004, you wrote: > >Dear all, > > > >I have been using the heatmap function to visualise my data and would > >like to obtain a list of my genes in the same order that > they appear in > >the heatmap. I have looked through the mail archives and tried just > >creating a dendogram and using order.dendogram but have so far been > >unsuccessful. Can anyone point me in the right direction? > > > >cheers > > > >claire > > > >-------------------------------------------------------- > > > > > >This email is confidential and intended solely for the use > o...{{dropped}} > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}} _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
0
14.5 years ago by
Francois Pepin1.3k
Francois Pepin1.3k wrote:
Hi everyone, we've been looking at something similar to try to pick single a series of genes from the heatmap. Based on Michael's suggestion: d <- dist(mydata) hc <- hclust(d) heatmap(mydata, RowV=as.dendrogram(hc)) genes<-identify(hc) So you can select the branch(es) of interest on the dendogram and get back the list of genes selected. Francois On Thu, 2004-11-04 at 09:06, Claire Wilson wrote: > Dear all, > > I have been using the heatmap function to visualise my data and would > like to obtain a list of my genes in the same order that they appear in > the heatmap. I have looked through the mail archives and tried just > creating a dendogram and using order.dendogram but have so far been > unsuccessful. Can anyone point me in the right direction? > > cheers > > claire > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use o...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor