search for: dendextend

Dear Martin, You are right. When implementing the dendextend::set function, I failed to notice that edgePar should accept a list instead of a vector. So all I did was to discover a bug in my own code. I am both sorry for taking your time due to my own mistake, and also grateful for your help (I will resolve this bug before submitting the next release to CRA...

...hile also allowing control over line types. I say this is clearly a bug in the code that messed up the dendrogram, see below. > This e-mail includes an example, and what I think a solution might be. > Reproducible example: > ================= > install.packages('dendextend') > library('dendextend') > dend <- 1:2 %>% dist %>% hclust %>% as.dendrogram > plot(dend) # works fine > dend %>% set("branches_lty", 1:2) %>% plot # works fine > dend %>% set("branches_col", 1:2) %>% plot...

Following "Introduction to dendextend" from Tal Galili, I applied this code on iris data: ## library(dendextend) library(dendextendRcpp) library(ggplot2) dend2 <- iris[1:30,-5] %>% dist %>% hclust %>% as.dendrogram %>% set("branches_k_color", k=3) %>% set("branches_lwd", rep(1,4)) %>% set(&...

...ULL, h = NULL,...) { UseMethod("cutree") } cutree.hclust <- stats::cutree # This will obviously need the actual content of stats::cutree This would be nicer for people like me to add new methods to cutree. For example the cutree.dendrogram function <https://github.com/talgalili/dendextend/blob/master/R/cutree.dendrogram.R> I implemented in dendextend, With regards, Tal [[alternative HTML version deleted]]

...n an error. I say this is a bug because (I believe), we would like a dendrogram to be able to use character colors, while also allowing control over line types. This e-mail includes an example, and what I think a solution might be. Reproducible example: ================= install.packages('dendextend') library('dendextend') dend <- 1:2 %>% dist %>% hclust %>% as.dendrogram plot(dend) # works fine dend %>% set("branches_lty", 1:2) %>% plot # works fine dend %>% set("branches_col", 1:2) %>% plot # works fine dend %>% set("branches_...

Hi all, This is the first time I'm writing to R-devel, and this time I'm just asking for the purpose for a certain line of code in stats::as.hclust.dendrogram, which comes up as I'm trying to fix dendextend. The line in question is at line 128 of dendrogram.R in R-3.3.3, at stats::as.hclust.dendrogram: stopifnot(length(s) == 2L, all( vapply(s, is.integer, NA) )) Is there any legitimate possibility that s is a nested list? Currently I have a case where a dendrogram object is breaks at this line, bec...

Note that cophenetic.default (which works on the output of hclust(dist(X))) uses the row names of X as labels. as.dendrogram.hclust does not retain those row names so cophenetic.dendrogram cannot use them (so it orders them based on the topology of the dendrogram). Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:

...still working on a robust benchmark. Suggestions for the best way to do that are welcome. - Support for applying functions with an inorder traversal (as in `stats::dendrapply`) as well as using a postorder traversal. This implementation was tested manually as well as running all the unit tests in `dendextend`, which comprises a lot of applications of `dendrapply`. The postorder traversal would be a significant new functionality to dendrapply, as it would allow for functions that use the child nodes to correctly execute. A toy example of this is something like: ``` exFunc <- function(x){ attr(x, &...