Hi, I'm experimenting with using GOstats, trying to draw graphs with Rgraphviz. If I follow the example in oneGOGraph.html I get a graph which is just circles and arrows, but no labels on the nodes. The plot functions gives warnings "Label GO:0003680 is too large for node in: drawTxtLabel ..." as below. Does anyone have any suggestions as to how I could get labels on the graph ? Regards, Mike Pheasant. > library(GOstats) Loading required package: graph Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: GO > g1 <- oneGOGraph("GO:0003680", GOMFPARENTS) > g2 <- oneGOGraph("GO:0003701", GOMFPARENTS) > g3 <- combGOGraph(g1, g2) > > if( require(Rgraphviz) && interactive() ) + plot(g3) Loading required package: Rgraphviz Creating a new generic function for "lines" in ".GlobalEnv" Creating a new generic function for "plot" in ".GlobalEnv" Warning messages: 1: X11 used font size 8 when 9 was requested 2: X11 used font size 8 when 7 was requested 3: Label GO:0003680 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 4: Label GO:0003677 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 5: Label GO:0003676 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 6: Label GO:0005488 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 7: Label GO:0003674 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 8: Label GO:0003673 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 9: Label GO:0003701 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName, 10: Label GO:0030528 is too large for node in: drawTxtLabel(txtLabel(node), nodeX, nodeY, width = rad * 2, nodeName,

> I'm experimenting with using GOstats, trying to draw graphs with > Rgraphviz. If I follow the example in oneGOGraph.html I get a graph > which is just circles and arrows, but no labels on the nodes. > The plot functions gives warnings "Label GO:0003680 is too large for > node in: drawTxtLabel ..." as below. > > Does anyone have any suggestions as to how I could get labels on the > graph ? Really the only way is to make sure that your nodes are plotted larger (either from increasing the size of the plot device or using less nodes). What happens is that Rgraphviz will first try to display the label at the default size, but if that would be too large it tries any smaller font sizes available. If none of them are small enough, instead of plotting the node/label such that the label is too large for the node, it gives the warning that you're seeing. -J