Question: heatmap and cluster with marray
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11.1 years ago by
Abhilash Venu340
Abhilash Venu340 wrote:
Hi all, As a part of my learning, I am trying to create a heatmap of differentially regulated genes. For the same I read the result of the 4 cases using 'read.table' and converted it into numerical matrix. Following this I created a distance matrix using the following command. EDistances<-dist(x,method = "euclidean") Clustering<-hclust(EDistances,method="complete") Followed by this I used 'marray' package for creating a heatmap using the following commands. >pal<-maPalette(low="green", high="red", mid="black") # I prefer this pattern, as it is looking good. > maColorBar(seq(-3,3, 0.5), col=pal, horizontal=FALSE, k=10) I used the following commands for creating the hierarchical cluster and heatmap. > EDistancesS<-dist(t(x),method = "euclidean") > ClusteringS<-hclust(EDistancesS,method="complete") > heatmap(x,Colv=as.dendrogram(ClusteringS),Rowv=as.dendrogram(Cluster ing), cexCol =0.8,col=pal,cexRow=1) But I am facing problem with the scale of color intensity. Such as I am not getting the intensity (scale or color key) in one graph itself. What could be the best method to resolve this problem and to create a heatmap with a properly defined color key in the same graph? Regards, Abhilash [[alternative HTML version deleted]]
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modified 11.1 years ago by Sean Davis21k • written 11.1 years ago by Abhilash Venu340
Answer: heatmap and cluster with marray
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11.1 years ago by
Artur Veloso340
Artur Veloso340 wrote:
Hi Abhilash, you might want to try the function heatmap.2 in the package gtools. I think this site might be useful: http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/he atmap/ Cheers, Artur On Wed, May 21, 2008 at 9:24 AM, Abhilash Venu <abhivenu@gmail.com> wrote: > Hi all, > > As a part of my learning, I am trying to create a heatmap of > differentially > regulated genes. For the same I read the result of the 4 cases using > 'read.table' and converted it into numerical matrix. Following this I > created a distance matrix using the following command. > > EDistances<-dist(x,method = "euclidean") > Clustering<-hclust(EDistances,method="complete") > > Followed by this I used 'marray' package for creating a heatmap using the > following commands. > >pal<-maPalette(low="green", high="red", mid="black") # I prefer this > pattern, as it is looking good. > > maColorBar(seq(-3,3, 0.5), col=pal, horizontal=FALSE, k=10) > I used the following commands for creating the hierarchical cluster and > heatmap. > > EDistancesS<-dist(t(x),method = "euclidean") > > ClusteringS<-hclust(EDistancesS,method="complete") > > heatmap(x,Colv=as.dendrogram(ClusteringS),Rowv=as.dendrogram(Clust ering), > cexCol =0.8,col=pal,cexRow=1) > > > But I am facing problem with the scale of color intensity. Such as I am not > getting the intensity (scale or color key) in one graph itself. What could > be the best method to resolve this problem and to create a heatmap with a > properly defined color key in the same graph? > > > Regards, > Abhilash > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
Answer: heatmap and cluster with marray
0
11.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, May 21, 2008 at 9:24 AM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > Hi all, > > As a part of my learning, I am trying to create a heatmap of differentially > regulated genes. For the same I read the result of the 4 cases using > 'read.table' and converted it into numerical matrix. Following this I > created a distance matrix using the following command. > > EDistances<-dist(x,method = "euclidean") > Clustering<-hclust(EDistances,method="complete") > > Followed by this I used 'marray' package for creating a heatmap using the > following commands. >>pal<-maPalette(low="green", high="red", mid="black") # I prefer this > pattern, as it is looking good. >> maColorBar(seq(-3,3, 0.5), col=pal, horizontal=FALSE, k=10) > I used the following commands for creating the hierarchical cluster and > heatmap. >> EDistancesS<-dist(t(x),method = "euclidean") >> ClusteringS<-hclust(EDistancesS,method="complete") >> heatmap(x,Colv=as.dendrogram(ClusteringS),Rowv=as.dendrogram(Cluste ring), > cexCol =0.8,col=pal,cexRow=1) > > > But I am facing problem with the scale of color intensity. Such as I am not > getting the intensity (scale or color key) in one graph itself. What could > be the best method to resolve this problem and to create a heatmap with a > properly defined color key in the same graph? Hi, Abhilash. You can try using the built-in help capabilities to get some hints. Try: help.search('heatmap') There are numerous methods for heatmaps available. Also, searching the email list archives will turn up even more hits. As a short answer, try the heatmap.2() function. Sean