plotMAhex               package:hexbin               R Documentation

_M_A-_p_l_o_t _u_s_i_n_g _h_e_x_a_g_o_n _b_i_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Creates an MA-plot using hexagons with color/glyph coding for
     control spots.

_U_s_a_g_e:

     plotMAhex(MA, array = 1, xlab = "A", ylab = "M",
               main = colnames(MA)[array], xlim = NULL, ylim = NULL,
               status, values, pch, col, cex, nbin = 40, zero.weights = FALSE,
               style = "colorscale", legend = 1.2, lcex = 1,
               minarea = 0.04, maxarea = 0.8, mincnt = 2, maxcnt = NULL,
               trans = NULL, inv = NULL, colorcut = NULL,
               border = NULL, density = NULL, pen = NULL,
               colramp = function(n) { LinGray(n, beg = 90, end = 15) },
               newpage = TRUE, type = c("p", "l", "n"),
               xaxt = c("s", "n"), yaxt = c("s", "n"),
               verbose = getOption("verbose"))

_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', 'Affybatch' or
          'exprSet' object

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

xlab, ylab, main: character strings giving label for x-axis, y-axis or
          main tile of the plot.

xlim, ylim: numeric vectors of length 2 giving limits for x-axis (or
          y-axis respectively), defaulting 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.

    nbin: ~~Describe 'nbin' here~~ 

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

   style: string specifying the style of hexagon plot, see
          'grid.hexagons' for the possibilities.

  legend: numeric width of the legend in inches of 'FALSE'. In the
          latter case, or when '0', no legend is not produced.

    lcex: characters  expansion size for the text in the legend

 minarea: fraction of cell area for the lowest count

 maxarea: fraction of the cell area for the largest count

  mincnt: cells with fewer counts are ignored.

  maxcnt: cells with more counts are ignored.

   trans: 'function' specifying a transformation for the counts such as
          'sqrt'.

     inv: the inverse transformation of 'trans'.

colorcut: vector of values covering [0, 1] that determine hexagon color
          class boundaries and hexagon legend size boundaries.
          Alternatively, an integer ('<= maxcnt') specifying the
          _number_ of equispaced colorcut values in [0,1].

border, density, pen: color for polygon borders and filling of each
          hexagon drawn, passed to 'grid.hexagons'.

 colramp: function accepting an integer 'n' as an argument and
          returning n colors.

 newpage: should a new page start?.

type, xaxt, yaxt: strings to be used (when set to '"n"') for
          suppressing the plotting of hexagon symbols, or the x- or
          y-axis, respectively.

 verbose: logical indicating if some diagnostic output should happen.

_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
     arrays, 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' from package 'limma' 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. and a list with
     the folowing items is returned invisibly: 

 plot.vp: the 'hexViewport' constructed and used.

legend.vp: if a legend has been produced, its 'viewport'.

    hbin: a 'hexbin' object built with A as the x coordinate and M as
          the y coordinate.

_A_u_t_h_o_r(_s):

     Nicholas Lewin-Koh, adapted from code by 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:

     'plotMA' from package 'limma', and 'gplot.hexbin'.

_E_x_a_m_p_l_e_s:

       if(require(marray)){ 
         data(swirl)
         hb <- plotMAhex(swirl[,1],newpage=FALSE,
                         main = "M vs A plot with hexagons", legend=0)
         hexVP.abline(hb$plot.vp,h=0,col=gray(.6))
         hexMA.loess(hb)
       }

