volcanoplot              package:limma              R Documentation

_V_o_l_c_a_n_o _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Creates a volcano plot of log-fold changes versus log-odds of
     differential expression.

_U_s_a_g_e:

     volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, xlab="Log Fold Change", ylab="Log Odds", pch=16, cex=0.35, ...)

_A_r_g_u_m_e_n_t_s:

     fit: an 'MArrayLM' fitted linear model object

    coef: integer giving the coefficient

highlight: number of top genes to be highlighted

   names: character vector giving text labels for the probes to be used
          in highlighting

    xlab: character string giving label for x-axis

    ylab: character string giving label for y-axis

     pch: vector or list of plotting characters. Default is integer
          code 16 which gives a solid circle.

     cex: numeric vector of plot symbol expansions. Default is 0.35.

     ...: any other arguments are passed to 'plot'

_D_e_t_a_i_l_s:

     A volcano plot is any plot which displays fold changes versus a
     measure of statistical significance of the change.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of presentation plots following the fitting of a
     linear model in LIMMA is given in 06.LinearModels.

_E_x_a_m_p_l_e_s:

     #  See lmFit examples