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 'exprSet'
          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 to integer
          code 16. 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 'exprSet' 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

_S_e_e _A_l_s_o:

     An overview of diagnostic functions available in LIMMA is given in
     7.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")

