writeReport             package:cellHTS             R Documentation

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_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)))

