plotBasic               package:BGmix               R Documentation

_B_a_s_i_c _p_l_o_t_s _o_f _B_G_m_i_x _p_a_r_a_m_e_t_e_r_s _a_n_d _d_a_t_a.

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

     Plots gene effects and variances versus their corresponding data
     sufficient statistics (to show the effect of smoothing and
     shrinkage). Also plots "volcano plots": posterior probabilities of
     being classified in  each mixture component versus the log fold
     change parameters.

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

     plotBasic(res, ybar, ss, q.mean = T, q.diff = T, q.sig = T, q.volcano = T)

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

     res: list object output from 'ccParams'

    ybar: ybar data (see 'BGmix' help for details)

      ss: ss data (see 'BGmix' help for details)

  q.mean: logical. Include mean plot?

  q.diff: logical. Include log fold change plot?

   q.sig: logical. Include variance plot?

q.volcano: logical. Include volcana plot (posterior classification v.
          fold change)? 

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

     Note this plotting function is designed for model output from the
     unpaired differential expression design.

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

     No value is returned to R. Results from BGmix model are output to
     files.

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

     Alex Lewin

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

     ## Note this is a very short MCMC run!
     ## For good analysis need proper burn-in period.
     data(ybar,ss)
     outdir <- BGmix(ybar, ss, c(8,8), nburn=0, niter=100, nthin=1)
     params <- ccParams(outdir)
     plotBasic(params,ybar,ss)

