plotPlateLibrary           package:cellHTS           R Documentation

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

     Given a 'cellHTS' object with data from an assay where every set
     of four consecutive 96-well plates was combined into a 384-well
     plate, this function plots the raw intensities of a chosen
     384-well assay plate distributed according to the 96-well plate
     format.

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

     plotPlateLibrary(x, whichPlate = 1, whichChannel = 1, plotSd = TRUE, plotPlateArgs)

_A_r_g_u_m_e_n_t_s:

       x: a cellHTS object containing the slot 'libPlate' with the
          96-well plate identifiers (see 'getLibraryPlate').

whichPlate: a number indicating the 384-well plate that we want to
          examine. (By default, it considers the first plate,
          'whichPlate = 1').

whichChannel: a number indicating the channel that we want to consider.
          (By default, the first channel is considered: 'whichChannel =
          1')

  plotSd: a logical value indicating whether the standard deviation
          across replicates should be plotted (default is 'plotSd =
          TRUE'.

plotPlateArgs: optional argument. If given, should be a list with
          parameters for the plate plots. See details.

_D_e_t_a_i_l_s:

     The cellHTS object 'x' contains data from a screening experiment
     where every set of four consecutive 96-well plates was combined
     into a 384-well plate. The plate identifiers for the 96-well
     plates are given in the slot 'libPlate', obtained by
     'getLibraryPlate'.

     Given the channel specified by 'whichChannel' and the 384-well
     plate number 'whichPlate', the function plots the raw intensities
     for each replicate in both the 96-well and the 384-well plate
     format. If 'plotSd = TRUE', the standard deviation across
     replicates is also plotted.

     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.

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

     Ligia Braz ligia@ebi.ac.uk

_S_e_e _A_l_s_o:

     'plotPlate', 'getLibraryPlate'

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

         data(KcViabSmall)
         x <- getLibraryPlate(KcViabSmall) 
         plotPlateLibrary(x, whichPlate=2, plotSd=TRUE)

