maPlot                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' produces scatter-plots of microarray spot
     statistics for the classes '"marrayRaw"' and '"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:

     maPlot(m, x="maA", y="maM", z="maPrintTip", lines.func, text.func, legend.func, ...)

_A_r_g_u_m_e_n_t_s:

       m: Microarray object of class '"marrayRaw"' and '"marrayNorm"'.

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

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

       z: 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 'z' 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 'z', 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.

     ...: 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):

     Sandrine Dudoit, <URL: http://www.stat.berkeley.edu/~sandrine>.

_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)

     # - Default arguments
     maPlot(swirl)

     # Lowess fit using all spots
     maPlot(swirl, z=NULL, legend.func=NULL)

     # Loess fit using all spots
     maPlot(swirl, z=NULL, legend.func=maLegendLines(legend="All spots",col="green"), lines.func=maLoessLines(loess.args=list(span=0.3),col="green"))

     # Pre-normalization MA-plot for the Swirl 81 array, with the lowess fits for 
     # individual grid columns and 1% tails of M highlighted
     defs <- maDefaultPar(swirl[, 1], x = "maA", y = "maM", z = "maGridCol")
     legend.func <- do.call("maLegendLines", defs$def.legend)
     lines.func <- do.call("maLowessLines", c(list(TRUE, f = 0.3), defs$def.lines))
     text.func<-maText(subset=maTop(maM(swirl)[,1],h=0.01,l=0.01), labels="o", col="violet")
     maPlot(swirl[, 1], x = "maA", y = "maM", z = "maGridCol", lines.func=lines.func, text.func = text.func, legend.func=legend.func, main = "Swirl array 81: pre-normalization MA-plot")