plotKEGGgraph           package:KEGGgraph           R Documentation

_P_l_o_t _K_E_G_G _g_r_a_p_h _w_i_t_h _R_g_r_a_p_h_v_i_z

_D_e_s_c_r_i_p_t_i_o_n:

     The function provides a simple interface to Rgraphviz to render
     KEGG graph with custom styles.

     'KEGGgraphLegend' gives the legend of KEGG graphs

_U_s_a_g_e:

     plotKEGGgraph(graph, y = "neato", shortLabel = TRUE,
     useDisplayName=TRUE, nodeRenderInfo,  ...)
     KEGGgraphLegend()

_A_r_g_u_m_e_n_t_s:

   graph: A KEGG graph, by calling 'parseKGML2Graph' 

       y: the layout method, 'neato' by default 

shortLabel: logical, should be short label used instead of full node
          name?

useDisplayName: logical, should the labels of nodes rendered as the
          'display name' specified in the KGML file or render them
          simply with the node names?

nodeRenderInfo: List of node rendering info

     ...: Other functions passed to renderGraph, not implemented for
          now

_D_e_t_a_i_l_s:

     Users are not restricted to this function, alternatively you can
     choose other rendering functions.

_V_a_l_u_e:

     The graph after layout and rendering is returned.

_A_u_t_h_o_r(_s):

     Jitao David Zhang <URL: mailto:j.zhang@dkfz.de>

_E_x_a_m_p_l_e_s:

     opar <- par(ask=TRUE)
     sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
     gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
     subs <-  c("hsa:1432",edges(gR)$`hsa:1432`,"hsa:5778","hsa:5801","hsa:84867","hsa:11072","hsa:5606","hsa:5608","hsa:5494","hsa:5609")
     gR.sub <- subGraph(subs, gR)
     if(require(Rgraphviz))
       plotKEGGgraph(gR.sub)

     KEGGgraphLegend()
     par(opar)

