symbolsInteresting            package:XDE            R Documentation

_U_s_e_f_u_l _f_o_r _c_h_a_n_g_i_n_g _t_h_e _l_o_o_k _o_f _p_a_i_r_s _p_l_o_t_s _t_o _e_m_p_h_a_s_i_z_e
_c_o_n_c_o_r_d_a_n_t _o_r _d_i_s_c_o_r_d_a_n_t _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function can be used to order genes in a matrix by the rank
     of a statistic and provide different plotting symbols and colors
     for genes that exceed a certain threshold of the ranking
     statistic.

_U_s_a_g_e:

     symbolsInteresting(rankingStatistic, percentile = 0.9, colors = c("grey50", "royalblue"), symbols = c(".", "o"), size = c(3, 1), background = c("white", "grey70"))

_A_r_g_u_m_e_n_t_s:

rankingStatistic: Any numerical vector 

percentile: A percentile of the rankingStatistic - above which a gene
          would be classified as 'interesting'

  colors: character string of length 2: a color for genes not exceeding
          the percentile and a color for genes exceeding the thresold

 symbols: two plotting symbols (numeric or character): symbol for genes
          not exceeding percentile and symbol for genes exceeding
          percentile

    size: numeric vector of length 2: size of plotting symbol for genes
          not exceeding percentile and size of plotting symbol for
          genes exceeding percentile 

background: character vector of length 2: background color of plotting
          symbols for gene not exceeding percentile and for genes
          exceeding the percentile

_V_a_l_u_e:

   order: the order of the rankingStatistic

     pch: plotting symbols (same length as rankingStatistic)

     col: color of plotting symbols (same length as rankingStatistic)

      bg: background color of plotting symbols (same length as
          rankingStatistic)

     cex: size of plotting symbols (same length as rankingStatistic)

_A_u_t_h_o_r(_s):

     R. Scharpf

_E_x_a_m_p_l_e_s:

       data(expressionSetList)
       data(xmcmc)
       bes <- bayesianEffectSize(xmcmc)
       postAvg <- posteriorAvg(xmcmc)
       op.conc <- symbolsInteresting(rankingStatistic=postAvg[, "concordant"])
       graphics:::pairs(bes[op.conc$order, ], pch=op.conc$pch, col=op.conc$col, 
                        bg=op.conc$bg, upper.panel=NULL, cex=op.conc$cex)  

