writeReport             package:cellHTS             R Documentation

_C_r_e_a_t_e _a _d_i_r_e_c_t_o_r_y _w_i_t_h _H_T_M_L _p_a_g_e_s _o_f _l_i_n_k_e_d _t_a_b_l_e_s _a_n_d _p_l_o_t_s
_d_o_c_u_m_e_n_t_i_n_g _t_h_e _c_o_n_t_e_n_t_s _o_f _a  _c_e_l_l_H_T_S _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     Creates a directory with HTML pages of linked tables and plots
     documenting the contents of a  cellHTS object.

_U_s_a_g_e:

     writeReport(x, outdir=x$name, force=FALSE, plotPlateArgs=FALSE, imageScreenArgs=NULL)

_A_r_g_u_m_e_n_t_s:

       x: a cell HTS object.

  outdir: a character of length 1 with the output base directory.

   force: a logical value, determines the behavior of the function if
          'outdir' contains anything. If 'force' is 'TRUE', the
          function forcefully recursively removes the contents of
          'outdir' of it, otherwise it casts an error.

plotPlateArgs: either a list with parameters for the plate plots the
          per plate quality report pages, or a logical with value
          'FALSE'. If 'FALSE', the plate plots are omitted, this option
          is here because the production of the plate plots takes a
          long time. See details.

imageScreenArgs: a list with parameters for the function 'imageScreen'.
          See details.

_D_e_t_a_i_l_s:

     The following elements are recognized for 'plotPlateArgs' and
     passed on to 'plotPlate': 'sdcol', the color scheme for the
     standard deviation plate plot, 'sdrange', the sd range to which
     the colors are mapped, 'xcol', the color scheme for the intensity
     plate plot, 'xrange', the intensity range to which the colors are
     mapped. If an element is not specified, default values are used.

     The following elements are recognized for 'imageScreenArgs' and
     passed on to 'imageScreen': 'ar', aspect ratio, 'zrange', range.

_V_a_l_u_e:

     The function is called for its side-effect. It returns the
     character 'outdir' with the path to the output directory.

_A_u_t_h_o_r(_s):

     Ligia Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

_S_e_e _A_l_s_o:

     'plotPlate', 'imageScreen'

_E_x_a_m_p_l_e_s:

      datadir = system.file("KcViabSmall", package = "cellHTS")
      x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
      confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
      logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
      descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
      x = configure(x, confFile, logFile, descripFile)
      writeReport(x)
      x = normalizePlateMedian(x, zscore="-")
      x = summarizeReplicates(x, summary="min")
      writeReport(x, force=TRUE, plotPlateArgs = list(), imageScreenArgs=list(zrange=c(-4,4)))

