plot.imageMatrix         package:arrayMagic         R Documentation

_V_i_s_u_a_l_i_s_a_t_i_o_n _o_f _a _m_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     Visualisation of a data matrix, e.g. a matrix representing a two
     dimensional area, a matrix of distance or similarity scores, or
     any numeric matrix. Coloured boxes represent values, labels will
     be drawn inside the box.

_U_s_a_g_e:

     plot.imageMatrix(x, labelMatrix, zlim, separateZScale=FALSE, zScale=TRUE, colourRamp, reverseYaxis = TRUE, labels, xLabels, yLabels, width=8, height=7, labelMatrixTextScaling=0.7, plotOutput="standard", fileName, ...)

_A_r_g_u_m_e_n_t_s:

       x: data matrix, class 'matrix'; required; default missing

labelMatrix: matrix of labels of class 'array' of dim('x'); optional;
          default missing

    zlim: numeric vector; defines the maximal z-range of the plot;
          default missing

  zScale: logical; adds a scale to the plot; required; default TRUE

separateZScale: logical; extra plot of the scale; required; default
          FALSE

colourRamp: vector of colours; optional; default missing

reverseYaxis: logical; required; default 'TRUE'

  labels: vector of names corresponding to  a quadratic 'x'; optional;
          default missing

 xLabels: vector of names corresponding to the columns of 'x' overrides
          'labels'; optional; default missing

 yLabels: vector of names corresponding to the rows of 'x' overrides
          'labels'; optional; default missing

   width: graphics window width; required; default: 8

  height: graphics window height; required; default: 7

labelMatrixTextScaling: numeric; required; default: 0.7

plotOutput: character string specifying either "standard", "screen",
          "twoScreens", "pdf" or "win.metafile"; required; default:
          "standard"

fileName: character string specifying the file path and file name;
          optional; default missing

     ...: arguments are passed to 'image'(), for example 'xlab', 'ylab'
          (x- and y-axis label) and 'main' (plot title) and 'asp=1' to
          set the aspect ratio to 1

_D_e_t_a_i_l_s:

     If no labels are supplied, the dimnames of 'x' or if missing a
     simple numbering is used instead.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_E_x_a_m_p_l_e_s:

      plot.imageMatrix(x=matrix(c(3,4,4,3),nrow=2, ncol=2),labels=c("one","two"))
      ma <- matrix(c(0.3,0.01,0.7,0.1,0.5,0.3,1,0.5,01), nrow=3,ncol=3)
      class(ma) <- c("imageMatrix", "matrix")
      plot(ma, labelMatrix=ma,labels=c("one","two", "three"), zlim=c(0,1))
      ma <- matrix(c(0.3, 0.01, 0.7, 0.1, 0.5, 0.3, 1, 0.5, 1, 0, 1, 0), nrow = 4, ncol = 3, byrow=TRUE )
      class(ma) <- c("imageMatrix", "matrix")
      plot(ma, labelMatrix = ma, xLabels = c("one", "two", "three"), zlim=c(0,1))
      plot(ma, reverseYaxis=FALSE, labelMatrix = ma, xLabels = c("one", "two", "three"), zlim=c(0,1))



      

