pairs-methods              package:DEDS              R Documentation

_P_a_i_r_s _P_l_o_t _f_o_r _D_E_D_S _O_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'pairs-DEDS' produces pairs plots of statistics or p
     values for 'DEDS-class' objects.

_U_s_a_g_e:

     ## S3 method for class 'DEDS':
     pairs(x, subset=c(1:nrow(x$stats)), labels =
     colnames(x$stats[,-1]), logit = FALSE,
     diagonal = c("qqnorm", "boxplot", "density", "histogram", "none"),
     lower = c("cor", "none"), groups.by.deds = TRUE, thresh = 0.05, reg.line
     = NULL, smooth = FALSE, line.by.group = FALSE, diag.by.group = TRUE, lower.by.group =
     FALSE, col = palette(), pch = 1:n.groups, lwd = 1, legend.plot =
     length(levels(groups)) > 1, ...)

_A_r_g_u_m_e_n_t_s:

       x: An object of 'DEDS'.

  subset: A numeric vector indicating the subset of points to be
          plotted.

  labels: A character vector specifying the names of the variables.

   logit: A logical variable, if 'TRUE' the variables are logged,
          useful when plotting p values.

diagonal: A character string specifying the type of plot to be applied
          in the diagonal panels. 

            'diagonal="qqnorm"':     'qqnorm' on the diagonal
            'diagonal="boxplot"':    'boxplot' on the diagonal
            'diagonal="density"':    'density' on the diagonal
            'diagonal="histogram"':  'hist' on the diagonal
            'diagonal="none"':       no special plot will be applied on the diagonal

   lower: A character string specifying the function to be applied in
          the lower panels. 

            'lower="cor"':  absolute correlation will be put on the lower panel
            'none="cor"';   no special function will be applied

groups.by.deds: A logcial variable, if 'TRUE', points will be separated
          into groups according to their magnitude of q- or p-values by
          DEDS. 

  thresh: A numeric variable, if 'thresh'<1, it specifies the threshold
          of significance in differential expression (DE) for q- or 
          p-values of the DEDS object; default is set at 0.05. If 
          'thresh'>1, it specifies the number of top DE genes to be
          highlighted. 

reg.line: A function name specifying the type of regressio line to be
          plotted in the scatter plots. If 'reg.line=lm', linear
          regression line will be plotted; If 'reg.line=NULL', no
          regression line will be plotted in the scatter plot.

  smooth: A logical variable specifying if smooth regression lines will
          be plotted in the scatter plots. If 'smooth=TRUE', a 'lowess'
          line will be applied.

line.by.group: A logical variable specifying if the regression lines
          should be applied within groups.

diag.by.group: A logical variable specifying if the plot in the
          diagonal panels whould be applied groupwise.

lower.by.group: A logical variable, if 'lower.by.group=TRUE' and
          'lower="cor"', correlation coefficients will be calculated
          and printed separated according to groups in the lower
          panels.

     col: A specification for the colors to be used for plotting
          different groups, see 'par'.

     pch: A specification for the type of points to be used for
          plotting different groups, see 'par'.

     lwd: A specification for the width of lines to be used if lines
          are plotted; see 'par'.

legend.plot: A logical variable specifying if the legend will be
          plotted.

     ...: Extra parameters for plotting.

_D_e_t_a_i_l_s:

     The function 'pairs.DEDS' implements a S3 method of 'pairs' for
     'DEDS'. The 'DEDS' class is a simple list-based class to store
     DEDS results and it is usually created  by functions 'deds.pval',
     'deds.stat', 'deds.stat.linkC'. The list contains a "stat"
     component, which stores statistics or p values from various
     statistical tests. The function 'pairs.DEDS' extracts the "stat"
     component and produces a matrix of scatterplot.

     'pairs.DEDS' as a default highlights points (corresponding to
     genes) with adjusted p- or q-values less than a user defined
     threshold. The user can select among a series of options a plot
     for the diagonal panel; as a default, it produces a 'qqnorm' for
     each column in the "stat" matrix. Both the diagonal and lower
     panels can be stratified by specifying the 'diag.by.group' or
     'lower.by.group' arguments.

_A_u_t_h_o_r(_s):

     Yuanyuan Xiao, yxiao@itsa.ucsf.edu, 
      Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

_S_e_e _A_l_s_o:

     'deds.stat', 'deds.pval', 'deds.stat.linkC', 'hist.DEDS',
     'qqnorm.DEDS'

_E_x_a_m_p_l_e_s:

     X <- matrix(rnorm(1000,0,0.5), nc=10)
     L <- rep(0:1,c(5,5))

     # genes 1-10 are differentially expressed
     X[1:10,6:10]<-X[1:10,6:10]+1
     # DEDS
     d <- deds.stat.linkC(X, L, B=200)

     # pairs plot
     pairs(d)
     # plot regression line
     pairs(d, reg.line=lm, lwd=2)
     # histogram in the diagonal panel
     pairs(d, diagonal="hist")
     # boxplot on the diagonal panel and stratified
     pairs(d, diagonal="boxplot", diag.by.group=TRUE)

