dendrogram | 易学教程

Change Dendrogram leaves

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问题 I want to modify the properties of the leaves in a dendrogram produced from plot of an hclust object. Minimally, I want to change the colors, but any help you can provide will be appreciated. I did try to google the answer, but but every solution that I saw seemed alot harder than what I would have guessed. 回答1: A while ago, Joris Meys kindly provided me with this snippet of code that changes the color of leaves. Modify it to reflect your attributes. clusDendro <- as.dendrogram(Clustering)

horizontal dendrogram in R with labels

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I am trying to draw a dendrogram from the hclust function output. I hope the dendrogram is horizontally arranged instead of the default, which can be obtain by (for example) require(graphics) hc <- hclust(dist(USArrests), "ave") plot(hc) I tried to use as.dendrogram() function like plot(as.dendrogram(hc.poi),horiz=TRUE) but the result is without meaningful labels: If I use plot(hc.poi,labels=c(...)) which is without the as.dendrogram() , I can pass the labels= argument, but now the dendrogram is vertical instead of horizontal. Is there a way to simultaneously arrange the dendrogram

How to create a dendrogram with colored branches?

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I would like to create a dendrogram in R which has colored branches, like the one shown below. So far I used following commands to create a standard dendrogram: d <- dist(as.matrix(data[,29])) # find distance matrix hc <- hclust(d) # apply hirarchical clustering plot(hc,labels=data[,1], main="", xlab="") # plot the dendrogram How should I modify this code to obtain desired result ? Thanks in advance for your help. You could use the dendextend package, aimed for tasks such as this: # install the package: if (!require('dendextend')) install.packages('dendextend'); library('dendextend') ##

How to colour the labels of a dendrogram by an additional factor variable in R

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问题 I have produced a dendrogram after running hierarchical clustering analysis in R using the below code. I am now trying to colour the labels according to another factor variable, which is saved as a vector. The closest that I have come to achieving this is to colour code the branches using the ColourDendrogram function in the sparcl package. If possible, I would prefer to colour-code the labels. I have found answers to a similar questions at the following links Color branches of dendrogram

how to plot and annotate hierarchical clustering dendrograms in scipy/matplotlib

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问题 I'm using dendrogram from scipy to plot hierarchical clustering using matplotlib as follows: mat = array([[1, 0.5, 0.9], [0.5, 1, -0.5], [0.9, -0.5, 1]]) plt.subplot(1,2,1) plt.title("mat") dist_mat = mat linkage_matrix = linkage(dist_mat, "single") print "linkage2:" print linkage(1-dist_mat, "single") dendrogram(linkage_matrix, color_threshold=1, labels=["a", "b", "c"], show_leaf_counts=True) plt.subplot(1,2,2) plt.title("1 - mat") dist_mat = 1 - mat linkage_matrix = linkage(dist_mat,

How do I create a radial cluster like the following code-example in Python?

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问题 I've found several examples on how to create these exact hierarchies (at least I believe they are) like the following here stackoverflow.com/questions/2982929/ which work great, and almost perform what I'm looking for. [EDIT]Here's a simplified version of Paul's code, which now should be easier for someone to help get this into a radial cluster instead of this current cluster shape import scipy import pylab import scipy.cluster.hierarchy as sch def fix_verts(ax, orient=1): for coll in ax

Label and color leaf dendrogram

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问题 I am trying to create a dendrogram, were my samples have 5 group codes (act as sample name/species/etc but its repetitive). Therefore, I have two issues that a help will be great: How can I show the group codes in leaf label (instead of the sample number)? I wish to assign a color to each code group and colored the leaf label according to it (it might happen that they will not be in the same clade and by that I can find more information)? Is it possible to do so with my script to do so (ape