dendextend

问题 Does anyone have a method to adorn an R corrplot correlation plot with a dendrogram? 回答1: The closest solution I know of is to use a heatmap on a correlation matrix, for example you could also use gplots::heatmap.2. Here is how to do it using the heatmaply R package, which also offers an interactive interface where you can zoom-in and get a tooltip when hovering over the cells: # for the first time: # install.packages("heatmaply") library(heatmaply) my_cor <- cor(mtcars) heatmaply_cor(my_cor)

问题 Does anyone have a method to adorn an R corrplot correlation plot with a dendrogram? 回答1: The closest solution I know of is to use a heatmap on a correlation matrix, for example you could also use gplots::heatmap.2. Here is how to do it using the heatmaply R package, which also offers an interactive interface where you can zoom-in and get a tooltip when hovering over the cells: # for the first time: # install.packages("heatmaply") library(heatmaply) my_cor <- cor(mtcars) heatmaply_cor(my_cor)

问题 How could I add a label for some colored bars I've added in a dendrogram plot? The code bellow will show the two attempts I've done for aiming task, which is linking the value 1 to the color red and value 0 to color white in a label for the colored bars. # replacing the graphic window parameter so the color bars would fit par( oma = c(0,1,1,1), mgp = c(1,0.5,0), mar = c(10,2,2,2) ) # load necessary packages library( squash ) library( dendextend ) # "initializatin" data("mtcars") myDend <- as

问题 How could I add a label for some colored bars I've added in a dendrogram plot? The code bellow will show the two attempts I've done for aiming task, which is linking the value 1 to the color red and value 0 to color white in a label for the colored bars. # replacing the graphic window parameter so the color bars would fit par( oma = c(0,1,1,1), mgp = c(1,0.5,0), mar = c(10,2,2,2) ) # load necessary packages library( squash ) library( dendextend ) # "initializatin" data("mtcars") myDend <- as

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 a numeric matrix in R with 24 rows and 10,000 columns. The row names of this matrix are basically file names from which I have read the data corresponding to each of the 24 rows. Apart from this I have a separate factor list with 24 entires, specifying the group to which the 24 files belong. There are 3 groups - Alcohols, Hydrocarbon and Ester. The names and the corresponding group to which they belong look like this: > MS.mz [1] "int-354.19" "int-361.35" "int-368.35" "int-396.38" "int

问题 I have done a Heat Map using the function heatmap.2 of gplots in R, but I don't have an idea of how to coloring the branches and tick labels per groups (Eg. if I cut the tree to have four gruops like in my second figure). I have checked that it is possible to color the dendrogram alone using dendextend package. Also there is a heatmap here: selecting number of leaf nodes of dendrogram in heatmap.2 in R with a colored dendrogram, but I can't implement it in my example. Somebody can help me

问题 I clustered my hclust() tree into several groups with cutree(). Now I want a function to hclust() the several groupmembers as a hclust()... ALSO: I cut one tree into 168 groups and I want 168 hclust() trees... My data is a 1600*1600 matrix. My data is tooooo big so I give you an example m<-matrix(1:1600,nrow=40) #m<-as.matrix(m) // I know it isn't necessary here m_dist<-as.dist(m,diag = FALSE ) m_hclust<-hclust(m_dist, method= "average") plot(m_hclust) groups<- cutree(m_hclust, k=18) Now I

问题 Initially I was trying to add the horizontal color side bar to the dendrogram plot (NOT to the whole heat map) using colored_bars from dendextend. The code below (THANK YOU for your help Tal!) works pretty well. The only issue remaining is how to control the distance of the bar from the leaves labels and the bar width? Here is an example, data and code Data (4 variables, 5 cases) df <- read.table(header=T, text="group class v1 v2 1 A 1 3.98 23.2 2 A 2 5.37 18.5 3 C 1 4.73 22.1 4 B 1 4.17 22.3