plotTrace               package:BGmix               R Documentation

_T_r_a_c_e _p_l_o_t_s _f_o_r _B_G_m_i_x _o_u_t_p_u_t.

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

     Trace plots are plotted for all scalar parameters. Optionally,
     traces are plotted for parameters indexed by genes, but for
     selected genes only.

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

     plotTrace(res, q.beta = T, q.sig = T, q.z = T, ind.genes = (1:3))

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

     res: list object output from 'ccTrace' 

  q.beta: logical. Plot trace of beta (gene effect) parameters?

   q.sig: logical. Plot trace of gene variances?

     q.z: logical. Plot trace of gene allocation parameters?

ind.genes: indices of genes for which to plot gene parameters.

_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)
     tr <- ccTrace(outdir)
     plotTrace(tr)
     plotTrace(tr,q.beta=TRUE,q.sig=FALSE,q.z=FALSE,ind.genes=1)
     plotTrace(tr,q.beta=FALSE,q.sig=FALSE,q.z=TRUE,ind.genes=sample(1:1000,5))

