search for: edgepar

Dear r-list, I am trying to visually seperate the two main clusters of a dendrogram. The idea is to use: 'edgePar=list(lty=3)' for 'dend1[[1]]' and 'edgePar=list(lty=1)' for 'dend1[[2]]' I have not found a way to solve this. Any suggestions? Patrick hc <- hclust(dist(USArrests), "ave") (dend1 <- as.dendrogram(hc)) par(mfrow=c(2,2)) plot(dend1) plot(dend1[[1]],edge...

...;str()" method str(dend1, max = 2) # only the first two sub-levels op <- par(mfrow= c(2,2), mar = c(5,2,1,4)) plot(dend1) ## "triangle" type and show inner nodes: plot(dend1, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8), type = "t", center=TRUE) plot(dend1, edgePar=list(col = 1:2, lty = 2:3), dLeaf=1, edge.root = TRUE) plot(dend1, nodePar=list(pch = 2:1,cex=.4*2:1, col = 2:3), horiz=TRUE) dend2 <- cut(dend1, h=70) plot(dend2$upper) ## leafs are wrong horizontally: plot(dend2$upper, nodePar=list(pch = c(1,7), col = 2:1)) ## dend2$lower is *NOT* a dendrogr...

...ul feature to have.... Or is there an easier way of doing this that I have missed? Walton Green * * * my.dend.plot <- function (x, type = c("rectangle", "triangle"), center = FALSE, edge.root = is.leaf(x) || !is.null(attr(x, "edgetext")), nodePar = NULL, edgePar = list(), leaflab = c("perpendicular", "textlike", "none"), dLeaf = NULL, xlab = "", ylab = "", xaxt = "n", yaxt = "s", horiz = FALSE, frame.plot = FALSE, twig.col = NULL, lab.col = NULL, leaf.col = NULL, ...){ ####...

...t;% plot # works fine # Fails: dend %>% set("branches_lty", 1:2) %>% set("branches_col", as.character(1:2)) %>% plot ### Error: # Error in segments(x0, y0, x1, y1, col = col, lty = lty, lwd = lwd) : # invalid line type: must be length 2, 4, 6 or 8 # This is because edgePar has to hold both "lty" and "col" # Since "col" is a character, it forces "lty" to become a character also. dend %>% set("branches_lty", 1:2) %>% set("branches_col", as.character(1:2)) %>% unclass %>% str Possible solution...

...rogram(hc)) plot(dend1) labels (USArrests) [[1]] # to know how many cities (labels) = 50 nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c("light blue", "pink"), lab.cex = 0.75, lab.col = 1:50) # or use a palette: palette(rainbow(50)) plot(dend1, edgePar=nP, dLeaf=1, edge.root = TRUE) # this option is not correct. I want each of my labels (text) have a different colour but that is not what is happening. How can I do that? I'd appreciate your help. thanks a lot again. Barbara On 9 December 2011 13:44, barbara costa <rbarbarahc@gmail.com&gt...

...ttr pipe mumbo-jumbo does not make it easy to deparse what you are doing ... and below you see why I think the bug is only in your 'dendextend' package. Please -- for supposed bugs in R, we do need reproducible examples *not* making use of external packages ! > # This is because edgePar has to hold both "lty" and "col" > # Since "col" is a character, it forces "lty" to become a character also. This is nonsense, sorry: If you'd read the help for plot.dendrogram(), edgePar is clearly defined as list, not vector, so it can well cont...

...8, lab.cex = 0.8)). But I got warning and the plot does not look like what I wanted. Warning messages: In plot.hclust(hc.obj, xlab = "", ylab = "", sub = "", nodePar = list(pch = c(1, : "nodePar" is not a graphical parameter It also can not recognize edgePar= dLeaf= edge.root Does someone know what's wrong? Br, Luffy

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 CRAN). I am sure that I would have had similar fee...

...;ave") plot(dend1) labels (USArrests) [[1]] # to know how many cities (labels) = 50 nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c("light blue", "pink"), lab.cex = 0.75, lab.col = 1:50) # or use a palette: palette(rainbow(50)) plot(dend1, edgePar=nP, dLeaf=1, edge.root = TRUE) # this option is not correct. I want each of my labels (text) have a different colour but that is not what is happening. How can I do that? I'd appreciate your help. thanks a lot Barbara [[alternative HTML version deleted]]

Hi all, Hi Gavin, thx for your help i finally found out what i want to do and how to fix it. just needed to get some more level my cut level was too small... two question remain... a) can i somehow scale the twigs after cutting ? b) how can i label the nodes and how to label which one... thx !! -m.

...r even in one orientation)? Alternatively, is there a way to modify the thickness and color of the edges that draw down from a "significant" node? I tried adding this to my markSignificantClusters() function, within the "if (nodesContainCertainLeaves)" block, to modify the edgePar settings of a qualifying node, to no effect: n <- dendrapply(n, function(e) { attr(e, "edgePar") <- list(lty=3, col="red"); e }) If you got this far through this message, thanks. :) I would be grateful for any advice. Thanks, Alex

...1[[2]][[1]] 1 ## use cNum attribute in "edgetext" ## following example in dendrogram documentation ## would really rather associate with the node than the edge ## but current plotting function has no notion of nodetext addE <- function(n) { if(!is.leaf(n)) { attr(n, "edgePar") <- list(p.col="plum") attr(n, "edgetext") <- attr(n,"cNum") } n } dend2 <- dendrapply(dend1, addE) ## overlays the cNum ("cluster number") attribute on dendrogram plot(dend2, main = "dend2") ## why does no plum polygon app...

...m' using an own function, and I'm using the R function plot.dendrogram for visualizing it. It works fine, but I could not find out how to change the font size of edge and leaf labels. ?plot.dendrogram has shown me that the coloring of the edge labels can be changed using plot(my.dendrogram, edgePar=list(t.col='green')), but something like 't.cex' doesn't seem to exist. Any hints greatly appreciated. Best regards, Michael

Using the heatmap function in mva, it seems to be hard to use different colors in the edges leading to different groups of objects, as commonly done in many heatmaps in the microarray graphics. Any suggestions? Thanks. max

...re preserved. o data.frame(check.names = TRUE) (the default) enforces unique names, as S does. o .Defunct() now has 'new' and 'package' arguments like those of .Deprecated(). o The plot() method for "dendrogram" objects now respects many more nodePar and edgePar settings and for edge labeling computes the extents of the diamond more correctly. o deparse(), dput() and dump() have a new 'control' argument to control the level of detail when deparsing. dump() defaults to the most detail, the others default to less. See ?.deparseOpts for the...

...re preserved. o data.frame(check.names = TRUE) (the default) enforces unique names, as S does. o .Defunct() now has 'new' and 'package' arguments like those of .Deprecated(). o The plot() method for "dendrogram" objects now respects many more nodePar and edgePar settings and for edge labeling computes the extents of the diamond more correctly. o deparse(), dput() and dump() have a new 'control' argument to control the level of detail when deparsing. dump() defaults to the most detail, the others default to less. See ?.deparseOpts for the...