dendrogram

问题 How do I draw a line in a dendrogram that corresponds the best K for a given criteria? Like this: Lets suppose that this is my dendrogram, and the best K is 4. data("mtcars") myDend <- as.dendrogram(hclust(dist(mtcars))) plot(myDend) I know that abline function is able to draw lines in graphs similarly to the one showed above. However, I don't know how could I calculate the height, so the function is used as abline(h = myHeight) 回答1: The information that you need to get the heights came with

问题 I have a heatmap (gene expression from a set of samples): set.seed(10) mat <- matrix(rnorm(24*10,mean=1,sd=2),nrow=24,ncol=10,dimnames=list(paste("g",1:24,sep=""),paste("sample",1:10,sep=""))) dend <- as.dendrogram(hclust(dist(mat))) row.ord <- order.dendrogram(dend) mat <- matrix(mat[row.ord,],nrow=24,ncol=10,dimnames=list(rownames(mat)[row.ord],colnames(mat))) mat.df <- reshape2::melt(mat,value.name="expr",varnames=c("gene","sample")) require(ggplot2) map1.plot <- ggplot(mat.df,aes(x=sample

问题 Using the function fviz_dend() of the factoextra package I created a dendogram that can be seen in the image at the end of the question. However, I cannot put the names of each species in italics. I tested the element_text(face = 'italic') function but it only works for the y-axis title. If anyone has any suggestions for leaving the species name in italics I thank. I believe it is something involving the fviz_dend() function but I have not found anything about it. Below it is possible to find

问题 I have a situation in which i am plotting a dendrogram with data points that come with class labels. I wish to see that agglomerative clustering groups those with the same label together. Color coding the labels makes it easy to read such a dendrogram. Is there a way we can achieve this with ggdendro in R ? 回答1: Stealing most of the setup from this post ... library(ggplot2) library(ggdendro) data(mtcars) x <- as.matrix(scale(mtcars)) dd.row <- as.dendrogram(hclust(dist(t(x)))) ddata_x <-

问题 I am trying to take my dataset which is made up of protein dna interaction, cluster the data and generate a heatmap that displays the resulting data such that the data looks clustered with the clusters lining up on the diagonal. I am able to cluster the data and generate a dendrogram of that data however when I generate the heatmap of the data using the heatmap function in R, the clusters are not visible. If you look at the first 2 images one is of the dendrogram I am able to generate, the

问题 I am trying to take my dataset which is made up of protein dna interaction, cluster the data and generate a heatmap that displays the resulting data such that the data looks clustered with the clusters lining up on the diagonal. I am able to cluster the data and generate a dendrogram of that data however when I generate the heatmap of the data using the heatmap function in R, the clusters are not visible. If you look at the first 2 images one is of the dendrogram I am able to generate, the

问题 I have to perform a cluster analysis on a big amount of data. Since I have a lot of missing values I made a correlation matrix. corloads = cor(df1[,2:185], use = "pairwise.complete.obs") Now I have problems how to go on. I read a lot of articles and examples, but nothing really works for me. How can I find out how many clusters are good for me? I already tried this: dissimilarity = 1 - corloads distance = as.dist(dissimilarity) plot(hclust(distance), main="Dissimilarity = 1 - Correlation",

问题 I have a data frame which I am trying to cluster. I am using hclust right now. In my data frame, there is a FLAG column which I would like to color the dendrogram by. By the resulting picture, I am trying to figure out similarities among various FLAG categories. My data frame looks something like this: FLAG ColA ColB ColC ColD I am clustering on colA , colB , colC and colD . I would like to cluster these and color them according to FLAG categories. Ex - color red if 1, blue if 0 (I have only

问题 I have a data frame which I am trying to cluster. I am using hclust right now. In my data frame, there is a FLAG column which I would like to color the dendrogram by. By the resulting picture, I am trying to figure out similarities among various FLAG categories. My data frame looks something like this: FLAG ColA ColB ColC ColD I am clustering on colA , colB , colC and colD . I would like to cluster these and color them according to FLAG categories. Ex - color red if 1, blue if 0 (I have only

问题 I have five points and I need to create dendrogram from these. The function 'dendrogram' can be used to find the ordering of these points as shown below. However, I do not want to use dendrogram as it is slow and result in error for large number of points (I asked this question here Python alternate way to find dendrogram). Can someone points me how to convert the 'linkage' output (Z) to the "dendrogram(Z)['ivl']" value. >>> from hcluster import pdist, linkage, dendrogram >>> import numpy >>>