plotMA                 package:limma                 R Documentation

_M_A-_P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Creates an MA-plot with color coding for control spots.

_U_s_a_g_e:

     plotMA(MA, array=1, xlab="A", ylab="M", main=colnames(MA)[array], xlim=NULL, ylim=NULL, status, values, pch, col, cex, legend=TRUE, zero.weights=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

      MA: an 'RGList', 'MAList' or 'MArrayLM' object, or any list with
          components 'M' containing log-ratios and 'A' containing
          average intensities. Alternatively a 'matrix' or
          'ExpressionSet' object.

   array: integer giving the array to be plotted. Corresponds to
          columns of 'M' and 'A'.

    xlab: character string giving label for x-axis

    ylab: character string giving label for y-axis

    main: character string giving title for plot

    xlim: numeric vector of length 2 giving limits for x-axis, defaults
          to min and max of the data

    ylim: numeric vector of length 2 giving limits for y-axis, defaults
          to min and max of the data

  status: character vector giving the control status of each spot on
          the array, of same length as the number of rows of 'MA$M'. If
          omitted, all points are plotted in the default color, symbol
          and size.

  values: character vector giving values of 'status' to be highlighted
          on the plot. Defaults to unique values of 'status'. Ignored
          if there is no 'status' vector.

     pch: vector or list of plotting characters. Default is integer
          code 16 which gives a solid circle. Ignored is there is no
          'status' vector.

     col: numeric or character vector of colors, of the same length as
          'values'. Defaults to '1:length(values)'. Ignored if there is
          no 'status' vector.

     cex: numeric vector of plot symbol expansions, of the the same
          length as 'values'.  Defaults to 0.2 for the most common
          status value and 1 for the others. Ignored if there is no
          'status' vector.

  legend: logical, should a legend of plotting symbols and colors be
          included. Ignored if there is no 'status' vector.

zero.weights: logical, should spots with zero or negative weights be
          plotted?

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

_D_e_t_a_i_l_s:

     An MA-plot is a plot of log-intensity ratios (M-values) versus
     log-intensity averages (A-values). If 'MA' is an 'RGList' or
     'MAList' then this function produces an ordinary within-array
     MA-plot. If 'MA' is an 'MArrayLM' object, then the plot is an
     fitted model MA-plot in which the estimated coefficient is on the
     y-axis and the average A-value is on the x-axis.

     If 'MA' is a 'matrix' or 'ExpressionSet' object, then this
     function produces a between-array MA-plot. In this case the
     A-values in the plot are the average log-intensities across the
     arrays and the M-values are the deviations of the log-intensities
     for the specified array from the average. If there are more than
     five arays, then the average is computed robustly using medians.
     With five or fewer arrays, it is computed by means.

     The 'status' vector is intended to specify the control status of
     each spot, for example "gene", "ratio control", "house keeping
     gene", "buffer" and so on. The vector is usually computed using
     the function 'controlStatus' and a spot-types file. However the
     function may be used to highlight any subset of spots.

     The 'status' can be included as the component 'MA$genes$Status'
     instead of being passed as an argument to 'plotMA'. The arguments
     'values', 'pch', 'col' and 'cex' can be included as attributes to
     'status' instead of being passed as arguments to 'plotMA'.

     See 'points' for possible values for 'pch', 'col' and 'cex'.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_R_e_f_e_r_e_n_c_e_s:

     See <URL: http://www.statsci.org/micrarra/refs/maplots.html>

_S_e_e _A_l_s_o:

     An overview of diagnostic functions available in LIMMA is given in
     09.Diagnostics.

_E_x_a_m_p_l_e_s:

     MA <- new("MAList")
     MA$A <- runif(300,4,16)
     MA$M <- rt(300,df=3)
     status <- rep("Gene",300)
     status[1:3] <- "M=0"
     MA$M[1:3] <- 0
     status[4:6] <- "M=3"
     MA$M[4:6] <- 3
     status[7:9] <- "M=-3"
     MA$M[7:9] <- -3
     plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"))

     #  Same as above
     attr(status,"values") <- c("M=0","M=3","M=-3")
     attr(status,"col") <- c("blue","red","green")
     plotMA(MA,main="MA-Plot with Simulated Data",status=status)

     #  Same as above
     MA$genes$Status <- status
     plotMA(MA,main="MA-Plot with Simulated Data")

