Dear BioC, I am rendering my own graph of gene ontology terms from my own 2 column matrix of nodes and nodes they are connected to, respectively. I am using the {graph} package command, ftM2graphNEL. Everything is working well and the results are very presentable until I try to manipulate attributes. If I plot the graph with the plot() method in {Rgrapgviz} with the graph object as the ONLY argument (everything else set as default), the graph is drawn in a very readable form and resembles any GO graph you see in the Bioconductor literature with "all" nodes eventually leading to the root node. However, when I change an attribute, say the fillcolor of the nodes using plot(myGraph, attrs = list(node = list(fillcolor = "yellow"))), the graph is rendered in a not-so readable format. It looks like all the nodes at each "generation" are flattened and separated into distinct rows. Regardless, does anyone know why my graph is being rendered differently after I set attributes? Thanks, Daniel Bornman Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229