termGraphs              package:GOstats              R Documentation

_E_x_t_r_a_c_t_i_o_n _a_n_d _P_l_o_t_t_i_n_g _o_f _G_O _T_e_r_m_s _f_r_o_m _a _G_O_H_y_p_e_r_G_R_e_s_u_l_t _O_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     These functions extract and plot 'graph' instances representing
     the relationships among GO terms tested using 'hyperGTest'.

_U_s_a_g_e:

     termGraphs(r, id = NULL, pvalue = NULL, use.terms = TRUE)
     inducedTermGraph(r, id, children = TRUE, parents = TRUE)
     plotGOTermGraph(g, r = NULL, add.counts = TRUE, max.nchar = 20,
                     node.colors=c(sig="lightgray", not="white"),
                     node.shape="plaintext", ...)

_A_r_g_u_m_e_n_t_s:

       r: A 'GOHyperGResult' object as returned by 'hyperGTest' when
          given a 'GOHyperGParams' object as input. 

      id: A character vector of category IDs that specifies which terms
          should be included in the graph.

  pvalue: Numeric p-value cutoff to use for selecting category terms to
          include.  Will be ignored if 'id' is present.

use.terms: Logical value indicating whether a '"term"' node attribute
          should be added to the returned graph providing the more
          descriptive, but possibly much longer, GO Terms.

children: A logical value indicating whether to include direct child
          terms of the terms specified by 'id'.

 parents: A logical value indicating whether to include direct parent
          terms of the terms specified by 'id'.

       g: A 'graph' object as returned by 'inducedTermGraph' or
          'termGraphs'.

add.counts: A logical value indicating whether category size counts
          should be added to the node labels when plotting.

max.nchar: The maximum character length for node labels in the plot.

node.colors: A named character vector of length two with compoents
          'sig' and 'not', giving color names for the significant and
          non-significant nodes, respectively.

node.shape: This argument controls the shape of the plotted nodes and
          must take on a value allowed by Rgraphviz.

     ...: For 'plotGOTermGraph', extra arguments are passed to the
          'plot' function.

_D_e_t_a_i_l_s:



     _t_e_r_m_G_r_a_p_h_s returns a list of 'graph' objects each representing one
          of the connected components of the subgraph of the GO
          ontology induced by selecting the specified GO IDs (if 'id'
          is present) or by selecting the GO IDs that have a p-value
          less that 'pvalue'.  If 'use.terms' is 'TRUE' the GO IDs will
          be translated into GO Term names and attached to the nodes as
          node attributes (see 'nodeData'). Edges in the graphs go from
          child (more specific) to parent (less specific).

     _i_n_d_u_c_e_d_T_e_r_m_G_r_a_p_h returns a 'graph' object representing the GO
          graph induced by the terms specified by 'id'.  The 'children'
          and 'parent' arguments control whether direct children and/or
          direct parents of the terms specified by 'id' are added to
          the graph (at least one of the two must be 'TRUE').

     _p_l_o_t_G_O_T_e_r_m_G_r_a_p_h Create a plot using Rgraphviz of a 'graph' object
          as returned by either 'termGraphs' or 'inducedTermGraph'.  If
          a 'GOHyperGResult' object is provided, then the nodes will be
          colored according to significance (based on the result
          object's 'pvalueCutoff') and counts will be added to show the
          size of the categories.


_A_u_t_h_o_r(_s):

     Seth Falcon

