plot.nem                 package:nem                 R Documentation

_p_l_o_t _n_e_s_t_e_d _e_f_f_e_c_t _m_o_d_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     plot graph of nested effects model, the marginal likelihood
     distribution or the posterior position of the effected genes

_U_s_a_g_e:

             ## S3 method for class 'nem':
             plot(x, what="graph", remove.singletons=FALSE, PDF=FALSE, filename="nemplot.pdf", thresh=0, transitiveReduction=FALSE, plot.probs=FALSE, SCC=TRUE, D=NULL, draw.lines=FALSE, palette="BlueRed",...)

_A_r_g_u_m_e_n_t_s:

       x: nem object to plot

    what: (i), "graph", (ii) "mLL" = likelihood distribution, (iii)
          "pos" = posterior position of effected genes

remove.singletons: remove unconnected nodes from the graph plot

     PDF: output as PDF-file

filename: filename of PDF-file

  thresh: if x has a real valued adjacency matrix (weight matrix), 
          don't plot edges with |weight| <= thresh

transitiveReduction: plot a transitively reduced graph

plot.probs: plot edge weights/probabilities. If regulation directions
          have been inferred (see 'infer.edge.type'), upregulated edges
          are drawn red and downregulated edges blue. Edges, were no
          clear direction could be inferred, are drawn in black.

     SCC: plot the strongly connected components graph

       D: Visualize the nested subset structure of the dataset via
          'plotEffects' along with the graph and show the linking of
          E-genes to S-genes in the dataset. Should only be used for
          small networks. Default: Just plot the graph

draw.lines: If the nested subset structure is shown, should
          additionally lines connecting S-genes and their associated
          E-genes be drawn? WARNING: For larger datasets than e.g. 5
          S-genes this most probably does not work, because the nested
          subset structure picture then partially overlaps with the
          graph picture. Default: Do not draw these lines

 palette: color palette to use: either 'BlueRed' (default) or 'Grey'

     ...: other arguments to be passed to the Rgraphviz plot function
          or to the graphics 'image' function.

_V_a_l_u_e:

     none

_A_u_t_h_o_r(_s):

     Florian Markowetz <URL: http://genomics.princeton.edu/~florian>,
     Holger Froehlich <URL: http://www.dkfz.de/mga2/people/froehlich>

_S_e_e _A_l_s_o:

     'nem', 'plotEffects', 'infer.edge.type'

