[BioC] PieGlyph - labels do not show

[Sim, Fraser]

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) || any(is.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) || any(is.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

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