search for: plotdendroandcolors

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 =

Dear R-Help, I have a clustering problem with hclust that I hope someone can help me with. Consider the classic hclust example: hc <- hclust(dist(USArrests), "ave") plot(hc) I would like to cut the tree up in such a way so as to avoid small clusters, so that we get a minimum number of items in each cluster, and therefore avoid singletons. e.g. in this example, you can see

...isc_3.9-3 [7] survival_2.36-14 flashClust_1.01-2 dynamicTreeCut_1.21 [10] impute_1.32.0 loaded via a namespace (and not attached): [1] grid_2.15.1 lattice_0.20-6 I have tried several methods for compiling the separate dendrograms together for the complete figure: Input: plotDendroAndColors(bwnet$dendrograms[[1:10]], bwModuleColors[bwnet$blockGenes[[1:10]]], "Module colors", dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05) # Above, 'bwnew$dendrograms[[x]]' is equivalent to the parameter speci...

...hich may be incorrect. The script I tried was: > dendro<-hclust(as.dist(combo2),method="average") > cut2<-cutreeDynamicTree(dendro,maxTreeHeight=1,deepSplit=TRUE,minModuleSize=1) I then used the following to visualise the data: > cut2colour<-labels2colors(cut2) > plotDendroAndColors(dendro,cut2colour,"Dynamic Tree Cut", > dendroLabels=FALSE,hang=0.03,addGuide=TRUE,guideHang=0.05) Any advice or ideas would be much appreciated! Thanks, Julia -- View this message in context: http://r.789695.n4.nabble.com/Grouping-clusters-from-dendrograms-tp2316521p2316521.html S...