plot                 package:marray                 R Documentation

_S_c_a_t_t_e_r-_p_l_o_t_s _f_o_r _c_D_N_A _m_i_c_r_o_a_r_r_a_y _s_p_o_t _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'maPlot' or 'plot' produces scatter-plots of
     microarray spot statistics for the classes '"marrayRaw"',
     '"marrayNorm"'. It also allows the user to highlight and annotate
     subsets of points on the plot, and display fitted curves from
     robust local regression or other smoothing procedures.

_U_s_a_g_e:

     plot.marrayRaw(x, xvar = "maA", yvar = "maM", zvar="maPrintTip", lines.func,text.func,legend.func,...)
     plot.marrayNorm(x, xvar = "maA", yvar = "maM", zvar="maPrintTip", lines.func,text.func,legend.func,...)
     addText(object, xvar="maA", yvar="maM", subset=NULL, labels=as.character(1:length(subset)), ...)
     addPoints(object, xvar="maA", yvar="maM", subset=TRUE, ...)
     addLines(object, xvar="maA", yvar="maM", zvar="maPrintTip", subset=TRUE, ...)
     ## S4 method for signature 'marrayRaw':
     text(x, xvar = "maA", yvar = "maM", ...)
     ## S4 method for signature 'marrayNorm':
     text(x, xvar = "maA", yvar = "maM", ...)
     ## S4 method for signature 'marrayRaw':
     lines(x, xvar = "maA", yvar = "maM", ...)
     ## S4 method for signature 'marrayNorm':
     lines(x, xvar = "maA", yvar = "maM", ...)
     ## S4 method for signature 'marrayRaw':
     points(x, xvar = "maA", yvar = "maM", ...)
     ## S4 method for signature 'marrayNorm':
     points(x, xvar = "maA", yvar = "maM", ...)

_A_r_g_u_m_e_n_t_s:

       x: Microarray object of class '"marrayRaw"', '"marrayNorm"'.

  object: Microarray object of class '"marrayRaw"', '"marrayNorm"'.

    xvar: Name of accessor function for the abscissa spot statistic,
          typically a slot name for the microarray object 'x', such as
          'maA'.

    yvar: Name of accessor function for the ordinate spot statistic,
          typically a slot name for the microarray object 'x', such as
          'maM'.

    zvar: Name of accessor method for the spot statistic used to
          stratify the data, typically a slot name for the microarray
          layout object (see '"marrayLayout"') such as 'maPlate' or a
          method such as 'maPrintTip'. If 'zvar' is NULL, the data are
          not stratified.

lines.func: Function for computing and plotting smoothed fits of 'y' as
          a function of 'x', separately within values of 'zvar', e.g.
          'maLoessLines'. If 'lines.func' is NULL, no fitting is
          performed.

text.func: Function for highlighting a subset of points, e.g.,
          'maText'. If 'text.func' is NULL, no points are highlighted.

legend.func: Function for adding a legend to the plot,  e.g.
          'maLegendLines'. If 'legend.func' is NULL, there is no
          legend.

  subset: logical vector or numeric values indicating the subset of
          points to be plotted.

  labels: One or more character strings or expressions specifying the
          text to be written.

     ...: Optional graphical parameters, see 'par'.

_D_e_t_a_i_l_s:

     This function calls the general function 'maPlot.func', which is
     not specific to microarray data. If there are more than one array
     in the batch, the plot is done for the first array, by default.
     Default graphical parameters are chosen for convenience using the
     function 'maDefaultPar' (e.g. color palette,  axis labels,  plot
     title) but the user has the option to overwrite these parameters
     at any point.

_A_u_t_h_o_r(_s):

     Jean Yee Hwa Yang

_R_e_f_e_r_e_n_c_e_s:

     S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data. In
     G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger,
     editors, _The Analysis of Gene Expression Data: Methods and
     Software_, Springer, New York.

_S_e_e _A_l_s_o:

     'maPlot.func', 'maDefaultPar', 'maLoessLines', 'maLegendLines',
     'maText', 'plot', 'lowess', 'loess', 'legend'.

_E_x_a_m_p_l_e_s:

     # To see the demo type demo(marrayPlots)

     # Examples use swirl dataset, for description type ? swirl
     data(swirl)

     # Pre-normalization MA-plot for the Swirl 93 array, with the lowess fits for 
     # individual print-tip-groups. 
     # - Default arguments
     plot(swirl[,3])

     # Lowess fit using all spots
     plot(swirl[,3], zvar=NULL, legend.func=NULL)

     # Loess fit using all spots
     plot(swirl[,3], zvar=NULL, legend.func=maLegendLines(legend="All spots",col="green"), lines.func=maLoessLines(loess.args=list(span=0.3),col="green"))