integrinMediatedCellAdhesion      package:graph      R Documentation

_K_E_G_G _I_n_t_e_g_r_i_n _M_e_d_i_a_t_e_d _C_e_l_l _A_d_h_e_s_i_o_n _g_r_a_p_h

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

     A graph representing the integrin-mediated cell adhesion pathway
     from KEGG, as well as a list of attributes for use in plotting the
     graph with 'Rgraphviz'.

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

     data(integrinMediatedCellAdhesion)

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

     The 'integrinMediatedCellAdhesion' data set contains two objects:

     The first is 'IMCAGraph', which is an object of class 'graph-NEL'
     and represents the hsa04510 graph from 'KEGG'.

     The second is 'IMCAAttrs', which is a list of four elements.  The
     first element, 'defAttrs' corresponds to the 'attrs' arguments of
     'agopen' and 'plot.graph'.  The second element is 'nodeAttrs'
     which corresponds to the 'nodeAttrs' argument in the same two
     functions from 'Rgraphviz'.  The third element, 'subGList'
     corresponds to the 'subGList' argument in those functions. 
     Lastly, the fourth element, 'LocusLink' provides a named list
     where the names are the nodes and the values are vectors of
     LocusLink ID values which correspond to those nodes.

     The values from 'defAttrs', 'nodeAttrs' and 'subGList' in the
     'IMCAAttrs' list are part of an ongoing attempt by Bioconductor to
     provide the set of options to most accurately recreate the actual
     visual image of the pathway from the KEGG site using 'Rgraphviz'. 
     Users may try out their own combination of attributes and settings
     for their own needs, but these represent our own efforts at as
     closely recreating the image as possible.

_S_o_u_r_c_e:

     <URL: http://www.genome.ad.jp/kegg/pathway/hsa/hsa04510.html>

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

     data(integrinMediatedCellAdhesion)
     if (require("Rgraphviz") & interactive())
       plot(IMCAGraph, attrs=IMCAAttrs$defAttrs,
            nodeAttrs=IMCAAttrs$nodeAttrs, subGList=IMCAAttrs$subGList)

