pheatmap

问题 Using pheatmap R package, I need to make a heatmap with annotations of a custom color set. I use the following code: ### Make a matrix mat<-replicate(23, rnorm(23)) colnames(mat)<-c("1","2","3plus3reseq","4","5","6","7","8","D1","D2","D3","11","12","13","14","15","16","59","e7","e8","e9","17","18") rownames(mat)<-c("1","2","3plus3reseq","4","5","6","7","8","D1","D2","D3","11","12","13","14","15","16","59","e7","e8","e9","17","18") ### Define annotations colData_D<-data.frame(time=factor(x=c

问题 Using pheatmap R package, I need to make a heatmap with annotations of a custom color set. I use the following code: ### Make a matrix mat<-replicate(23, rnorm(23)) colnames(mat)<-c("1","2","3plus3reseq","4","5","6","7","8","D1","D2","D3","11","12","13","14","15","16","59","e7","e8","e9","17","18") rownames(mat)<-c("1","2","3plus3reseq","4","5","6","7","8","D1","D2","D3","11","12","13","14","15","16","59","e7","e8","e9","17","18") ### Define annotations colData_D<-data.frame(time=factor(x=c

问题 I am using the R heatmaply package to produce interactive heatmaps. I like the software, but I would like to get from it the same clustering (ordering of rows and columns) I get using the pheatmap package. Therefore, I would like the two commands to produce the same ouput: heatmaply (scale (mtcars)) pheatmap (scale (mtcars)) Is there a way to do this? Thanks in advance. Arturo P.S. I recently asked another similar question about the color output, i.e., not clustering, output, that was

问题 I am trying to plot a heatmap with the library pheatmap in R. I think that by default the branch length is proportional to the "dissimilarity" of the clusters that got merged at this step. I would like to chance that, so it is a fixed value because for my purpose it looks very weird! If anyone has an idea how I can fix this, I would be very happy. Here is a sample code library(pheatmap) test = matrix(rnorm(6000), 100, 60) pheatmap(test) Cheers! 回答1: Here is an example of two column groups

来源： https://stackoverflow.com/questions/25495965/pheatmap-formatting-in-r-legend-size-and-creating-a-square-plot

来源： https://stackoverflow.com/questions/63944085/using-pheatmap-to-sort-data-by-row-annotations

来源： https://stackoverflow.com/questions/63944085/using-pheatmap-to-sort-data-by-row-annotations

来源： https://stackoverflow.com/questions/63833198/improving-my-heatmap-in-r-with-pheatmap

来源： https://stackoverflow.com/questions/63833198/improving-my-heatmap-in-r-with-pheatmap

问题 I am using the R heatmaply package to produce interactive heatmaps. I like the software, but I would like to get from it the same color output I get using the pheatmap package. Therefore, I would like the two commands to produce the same ouput: heatmaply (scale (mtcars)) pheatmap (scale (mtcars)) Is there a way to do this? Thanks in advance. Arturo 回答1: You can use formals() to get the default color argument of pheatmap() . formals(pheatmap)$color # colorRampPalette(rev(brewer.pal(n = 7, name