tweaks for the heatmap ()?
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Simon Lin ▴ 270
@simon-lin-1272
Last seen 8.4 years ago
I am looking for two tweaks of the heatmap function: 1) a choice to order the genes by 1-D MDS projection. The current hierarchical clustering flips many nodes. 2) a color bar at the side to indicate the color scale, as with maColorBar() in the marray package Any code to share? Thanks! Simon
Clustering marray Clustering marray • 1.1k views
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Florian Hahne ▴ 540
@florian-hahne-2471
Last seen 8.4 years ago
Simon Lin wrote: > I am looking for two tweaks of the heatmap function: > 1) a choice to order the genes by 1-D MDS projection. The current > hierarchical clustering flips many nodes. > 2) a color bar at the side to indicate the color scale, as with maColorBar() > in the marray package > > Any code to share? > > Thanks! > > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Hi Simon, you might want to take a look at the levelplot function in the lattice package. The following code snippet emulates what heatmap does with a colorbar added to the plot: myHeatmap = function(x) { dd.row = as.dendrogram(hclust(dist(x))) row.ord = order.dendrogram(dd.row) dd.col = as.dendrogram(hclust(dist(t(x)))) col.ord = order.dendrogram(dd.col) levelplot(x[row.ord,col.ord], scales = list(x = list(rot = 90)), xlab="", ylab="", main="whatever the title is" col.regions=colorRampPalette(c("white", "darkblue"))(256)) } You can use any ordering of the rows and column by modifying the assignments to row.ord and col.ord BW, Florian
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@james-w-macdonald-5106
Last seen 56 minutes ago
United States
Hi Simon, Have you looked at heatmap.2() in gplots? It will draw the color key. As for the gene ordering, you can always feed heatmap.2() (or heatmap(), for that matter) an ordered matrix of data based on the MDS projection and then set Rowv=NA to keep from reordering the genes. Or did you want no reordering, but some sort of a dendrogram as well? Best, Jim Simon Lin wrote: > I am looking for two tweaks of the heatmap function: > 1) a choice to order the genes by 1-D MDS projection. The current > hierarchical clustering flips many nodes. > 2) a color bar at the side to indicate the color scale, as with maColorBar() > in the marray package > > Any code to share? > > Thanks! > > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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Aedin Culhane ▴ 510
@aedin-culhane-1526
Last seen 3.4 years ago
United States
Dear Simon Also have a look at heatplot() in the package made4. It calls heatmap.2 . Input parameters include: dend="both", "row" or "column" or "row" By default it uses the blue-brown color scheme, 1-Pearson correlation distance, average linkage joining and will automatically draw a scale color-bar. It will automatically scale the row for better visualization. To view the real data values, use scale ="none" Regards Aedin
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