Hi Fraser, I just added your fix to Rgraphviz. The idea of the user-defined glyph drawing functions is that people can draw whatever they want to, e.g. by extending already available functions, but since the pieGlyph documentation is advertising labels I agree that it should deliver... Thanks for the patch, Florian Sim, Fraser wrote: > I fixed the problem by referring to pie function and editing pieGlyphs > accordingly. > > It's designed to draw lines +10% of the radius out for each label, and > place the labels +20% from the center. It seems to works ok. > > Can we somehow add this to Rgraphviz? > > Fraser > > Here's my code: > > pieGlyph_new = function (x, xpos, ypos, labels = names(x), edges = 200, > radius = 0.8, > density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, > main = NULL, ...) > { > if (!is.numeric(x) || anyis.na(x) | x <= 0)) > stop("pie: `x' values must be positive.") > if (is.null(labels)) > labels <- as.character(1:length(x)) > x <- c(0, cumsum(x)/sum(x)) > dx <- diff(x) > nx <- length(dx) > if (is.null(col)) > col <- if (is.null(density)) > c("lightblue", "mistyrose", "lightcyan", "lavender", > "cornsilk", "white") > else par("fg") > col <- rep(col, length.out = nx) > border <- rep(border, length.out = nx) > lty <- rep(lty, length.out = nx) > angle <- rep(angle, length.out = nx) > density <- rep(density, length.out = nx) > for (i in 1:nx) { > n <- max(2, floor(edges * dx[i])) > t2p <- 2 * pi * seq(x[i], x[i + 1], length = n) > xc <- c(cos(t2p), 0) * radius + xpos > yc <- c(sin(t2p), 0) * radius + ypos > polygon(xc, yc, density = density[i], angle = angle[i], > border = border[i], col = col[i], lty = lty[i]) > > # new code here > t2p <- 2 * pi * mean(x[i + 0:1]) > xc <- cos(t2p) * radius * c(1,1.1,1.2) + xpos > yc <- sin(t2p) * radius * c(1,1.1,1.2) + ypos > lab <- as.character(labels[i]) > if (!is.na(lab) && nzchar(lab)) { > lines(xc[1:2], yc[1:2]) > text(xc[3], yc[3], labels[i], xpd = TRUE, > adj = ifelse(xc < xpos, 1, ifelse(xc == xpos, 0.5, > 0)),...) > } > # end new code > > } > invisible(NULL) > } > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sim, Fraser > Sent: Thursday, April 16, 2009 4:09 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] PieGlyph - labels do not show > > Hi Robert, > > I'm working with RGraphViz to plot PieGlyphs and wanted to try and add > labels to the pie slices. The Usage page describes such a use. > > If I tried the following but no labels appear: > > library(Rgraphviz) > plot(1:10, col="white") > pieGlyph(1:2, 5, 5, labels = c("A","B") ) > > **************************************** > Also when I look at the function itself, it does look like it uses > 'labels' at all. > > function (x, xpos, ypos, labels = names(x), edges = 200, radius = 0.8, > density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, > main = NULL, ...) > { > if (!is.numeric(x) || anyis.na(x) | x <= 0)) > stop("pie: `x' values must be positive.") > if (is.null(labels)) > labels <- as.character(1:length(x)) > x <- c(0, cumsum(x)/sum(x)) > dx <- diff(x) > nx <- length(dx) > if (is.null(col)) > col <- if (is.null(density)) > c("lightblue", "mistyrose", "lightcyan", "lavender", > "cornsilk", "white") > else par("fg") > col <- rep(col, length.out = nx) > border <- rep(border, length.out = nx) > lty <- rep(lty, length.out = nx) > angle <- rep(angle, length.out = nx) > density <- rep(density, length.out = nx) > for (i in 1:nx) { > n <- max(2, floor(edges * dx[i])) > t2p <- 2 * pi * seq(x[i], x[i + 1], length = n) > xc <- c(cos(t2p), 0) * radius + xpos > yc <- c(sin(t2p), 0) * radius + ypos > polygon(xc, yc, density = density[i], angle = angle[i], > border = border[i], col = col[i], lty = lty[i]) > } > invisible(NULL) > } > <environment: namespace:rgraphviz=""> > > ****************************************** > > Here's my sessionInfo. > > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices datasets utils tools > > [8] methods base > > other attached packages: > [1] org.Hs.eg.db_2.2.6 bioDist_1.14.0 gplots_2.6.0 > [4] gdata_2.4.2 gtools_2.5.0 limma_2.16.4 > [7] RColorBrewer_1.0-2 hgu133plus2.db_2.2.5 RSQLite_0.7-1 > [10] DBI_0.2-4 AnnotationDbi_1.4.2 Rgraphviz_1.21.7 > [13] graph_1.20.0 Biobase_2.2.1 rcom_2.0-4 > [16] rscproxy_1.0-12 > > loaded via a namespace (and not attached): > [1] annotate_1.20.1 Category_2.8.2 cluster_1.11.12 > genefilter_1.22.0 > [5] GSEABase_1.4.0 KEGGgraph_0.8.15 RBGL_1.18.0 ROC_1.16.0 > > [9] splines_2.8.1 survival_2.34-1 XML_1.99-0 > > Thanks, > Fraser > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Florian Hahne, PhD Computational Biology Program Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-3148 fhahne at fhcrc.org