dendextend

Tree cut and Rectangles around clusters for a horizontal dendrogram in R

 ̄綄美尐妖づ 提交于 2019-11-29 03:07:56
问题 I am trying to plot the results of a hierarchical clustering in R as a dendrogram, with rectangles identifying clusters. The following code does the trick for a vertical dendrogram, but for a horizontal dendrogram, ( horiz=TRUE ), the rectangles are not drawn. Is there any way to do the same for horizontal dendrograms too. library("cluster") dst <- daisy(iris, metric = c("gower"), stand = FALSE) hca <- hclust(dst, method = "average") plot(as.dendrogram(hca), horiz = FALSE) rect.hclust(hca, k

Change Dendrogram leaves

与世无争的帅哥 提交于 2019-11-29 00:13:56
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. 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) labelColors <- c("red", "blue", "darkgreen", "darkgrey", "purple") ## function to get colorlabels colLab <-

How do you compare the “similarity” between two dendrograms (in R)?

天涯浪子 提交于 2019-11-28 21:12:40
问题 I have two dendrograms which I wish to compare to each other in order to find out how "similar" they are. But I don't know of any method to do so (let alone a code to implement it, say, in R). Any leads ? UPDATE (2014-09-13): Since asking this question, I have written an R package called dendextend, for the visualization, manipulation and comparison of dendrogram. This package is on CRAN and comes with a detailed vignette. It includes functions such as cor_cophenetic , cor_bakers_gamma and Bk

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

混江龙づ霸主 提交于 2019-11-28 11:23:51
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 using an existing column & Colouring branches in a dendrogram in R , but I have not been able to work out

Change Dendrogram leaves

落花浮王杯 提交于 2019-11-27 15:31:11
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)

How to create a dendrogram with colored branches?

南笙酒味 提交于 2019-11-27 09:17:05
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

痞子三分冷 提交于 2019-11-27 06:07:43
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

Label and color leaf dendrogram

左心房为你撑大大i 提交于 2019-11-26 07:39:25
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