search for: plotnode

Hi All, I've gotten a number of reports from users about gplots::heatmap.2 generating 'node stack overflow' errors. As it turns out, these errors originate in stats:::plotNode, and are triggered when it is passed a dendrogram that is too deeply nested. While increasing the stack size (which is a compile-time option for byte coded functions) can allow a particular instance to succeed, a better solution would be to modify stats:::plotNode to use a recursive, rather than i...

Hello, It seems that the plot function for dendrograms does not draw labels when they are too long. > hc <- hclust(dist(USArrests), "ave") > dend1 <- as.dendrogram(hc) > dend2 <- cut(dend1, h=70) > dd <- dend2$lower[[1]] > plot(dd) # first label is drawn > attr(dd[[1]], "label") <- "aaaaaaaaaaaaaaaaaa" > plot(dd) # first label is

...ot;none"), dLeaf = NULL, xlab = "", ylab = "", xaxt = "n", yaxt = "s", horiz = FALSE, frame.plot = FALSE, twig.col = NULL, lab.col = NULL, leaf.col = NULL, ...){ ############################## 80 Characters Wide ############################## plotNode <- function (x1, x2, subtree, type, center, leaflab, dLeaf, nodePar, edgePar, horiz = FALSE, leafcounter = leafcounter, ...) { #cat('.') uncomment this for debugging... inner <- !is.leaf(subtree) && x1 != x2 yTop <- attr(subtree, "height") bx &...

...y" to become a character also. dend %>% set("branches_lty", 1:2) %>% set("branches_col", as.character(1:2)) %>% unclass %>% str Possible solution ============== The simplest (and backward) compatible solution I can think of is to edit the function: stats:::plotNode And change the following lines: col <- Xtract("col", ePar, default = par("col"), i) lty <- Xtract("lty", ePar, default = par("lty"), i) lwd <- Xtract("lwd", ePar, def...

...; attr(d[[1]], "edgetext") <- "a & b" > attr(d[[2]], "edgetext") <- "c & d" > plot(d, horiz="F") #OK > plot(d, horiz="T") #edge labels do not change position to account for horiz I think this is because stats:::plotNode doesn't deal with horiz=TRUE on line 152 (starting "polygon(mx + c(-hl3, hl3),"). I'm quite happy to submit a patch to fix this, but I'm not sure how to do so. Is there a web page which gives details about the preferred format for patches, and how to download the latest...

...e colors'' just for fun) [ Currently, I don't see a bug in R's dendrogram code but rather in your package. > Possible solution > ============== > The simplest (and backward) compatible solution I can think of is to edit > the function: > stats:::plotNode > And change the following lines: > col <- Xtract("col", ePar, default = par("col"), > i) > lty <- Xtract("lty", ePar, default = par("lty"), > i) > lwd <- Xtract("lwd", ePar, default = par("lw...

...identify(). The frustrating thing is that when I do d <- dim(stuff))[1] plot(1:d, 1:d, col=col[stuff.hc$order]) shows me that there _is_ a strong connection between the groups found by hclust() and the predicted groups, albeit not a simple one. I have looked at plot.dendrogram() and plotNode() -- using getAnywhere() -- and it looks to me as though what I want *should* be doable, but I've clearly misunderstood the details of how to do it.

Hi, hres <- hclust(smatr,method="single") hresd<-as.dendrogram(hres) as.dendrogram(hres) `dendrogram' with 2 branches and 380 members total, at height 2514.513 plot(hresd,leaflab="none") #<-error here. #the plotted dendrogram is incomplete. The x axis is not drawn. #The interested reader can download the save(hresd,file="hres.rda") #from the

...ce environments to lists (efficiently). o New function addmargins() in the stats package to add marginal summaries to tables, e.g. row and column totals. (Based on a contribution by Bendix Carstensen.) o dendrogam edge and node labels can now be expressions (to be plotted via stats:::plotNode called from plot.dendrogram). The diamond frames around edge labels are more nicely scaled horizontally. o Methods defined in the methods package can now include default expressions for arguments. If these arguments are missing in the call, the defaults in the selected method will overri...

...ce environments to lists (efficiently). o New function addmargins() in the stats package to add marginal summaries to tables, e.g. row and column totals. (Based on a contribution by Bendix Carstensen.) o dendrogam edge and node labels can now be expressions (to be plotted via stats:::plotNode called from plot.dendrogram). The diamond frames around edge labels are more nicely scaled horizontally. o Methods defined in the methods package can now include default expressions for arguments. If these arguments are missing in the call, the defaults in the selected method will overri...