plotModel                package:qtl                R Documentation

_P_l_o_t _a _Q_T_L _m_o_d_e_l

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

     Plot a graphical representation of a QTL model, with nodes
     representing QTL and line segments representing pairwise
     interactions.

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

     plotModel(qtl, formula, circrad.rel=0.25, circrad.abs,
              cex.name=1, chronly=FALSE, order, ...)

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

     qtl: A QTL object (as created by 'makeqtl') or vector of character
          strings indicating the names for the QTL.  This is also
          allowed to be a list that contains a component named '"chr"'
          (and, optionally, components names '"pos"' and '"formula"').

 formula: Optional formula defining the QTL model.  If missing, we look
          for an attribute '"formula"' to the input QTL object or a
          item named '"formula"' within the QTL object.

circrad.rel: Radius of the circles that indicate the QTL, relative to
          the distance between the circles.

circrad.abs: Optional radius of the circles that indicate the QTL; note
          that the plotting region will have x- and y-axis limits
          spanning 3 units.

cex.name: Character expansion for the QTL names.

 chronly: If TRUE and a formal QTL object is given, only the chromosome
          IDs are used to identify the QTL.

   order: Optional vector indicating a permutation of the QTL to define
          where they are to appear in the plot.  QTL are placed around
          a circle, starting at the top and going clockwise.

     ...: Passed to the function 'plot'.

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

     None.

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

     Karl W Broman, kbroman@biostat.wisc.edu

_S_e_e _A_l_s_o:

     'stepwiseqtl', 'makeqtl'

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

     # plot a QTL model, using a vector of character strings to define the QTL
     plotModel(c("1","4","6","15"), formula=y~Q1+Q2+Q3*Q4)

     # plot an additive QTL model
     data(hyper)
     hyper <- calc.genoprob(hyper)
     qtl <- makeqtl(hyper, chr=c(1,4,6,15), pos=c(68.3,30,60,18), what="prob")
     plotModel(qtl)

     # include an interaction
     plotModel(qtl, formula=y~Q1+Q2+Q3*Q4)

     # alternatively, include the formula as an attribute to the QTL object
     attr(qtl, "formula") <- y~Q1+Q2+Q3*Q4
     plotModel(qtl)

     # if formula given, the attribute within the object is ignored
     plotModel(qtl, y~Q1+Q2+Q3+Q4)

     # NULL formula indicates additive QTL model
     plotModel(qtl, NULL)

     # reorder the QTL in the figure
     plotModel(qtl, order=c(1,3,4,2))

     # show just the chromosome numbers
     plotModel(qtl, chronly=TRUE)

