image.dev                package:xps                R Documentation

_I_m_a_g_e _f_o_r _D_e_v_i_c_e

_D_e_s_c_r_i_p_t_i_o_n:

     Creates an image for each sample for the selected device.

_U_s_a_g_e:

     image.dev(x, bg = FALSE, transfo = log2, col = gray((0:64)/64), names = "namepart", xlab = "", ylab = "", mar = c(1, 1, 2, 1), dev = "screen", outfile = "Image", w = 540, h = 540, ...)

_A_r_g_u_m_e_n_t_s:

       x: object of class 'DataTreeSet'.

      bg: logical. If 'FALSE', intensities from slot 'data' will be
          used; if 'TRUE', background intensities from slot 'bgrd' will
          be used.

 transfo: a valid function to transform the data, usually "log2", or
          "0".

     col: color range for intensities.

   names: optional vector of sample names.

    xlab: a title for the x axis.

    ylab: a title for the y axis.

     mar: plot margins.

     dev: graphics device to plot to, i.e. one of "screen",
          "jpeg","png", "pdf" or "ps".

 outfile: the name of the output file.

       w: the width of the device in pixels.

       h: the height of the device in pixels.

     ...: optional arguments to be passed to 'image'.

_D_e_t_a_i_l_s:

     Creates an image for each array for the selected graphics device.

     For 'bgrd=TRUE' the distribution of the computed background
     intensities will be shown; this can be useful to see potential
     density gradients caused by hybridization conditions. For the
     computation of background intensities see function 'bgcorrect'; it
     is suggested to use 'bgcorrect.mas4' to identify density
     gradients.

     For 'names=NULL' full column names of slot 'data' will be
     displayed while for  'names="namepart"' column names will be
     displayed without name extension. If 'names' is a vector of column
     names, only these columns will displayed as image.

_N_o_t_e:

     Data must first be attached to class 'DataTreeSet' using method
     'attachInten'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'image-methods', 'image'

_E_x_a_m_p_l_e_s:

     ## first, load ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     ## need to attach scheme mask and data
     data.test3 <- attachMask(data.test3)
     data.test3 <- attachInten(data.test3)

     if (interactive()) {
     image.dev(data.test3)
     }

     ## to avoid memory comsumption of R remove data:
     data.test3 <- removeInten(data.test3)
     data.test3 <- removeMask(data.test3)

