configurationAsScreenPlot      package:cellHTS2      R Documentation

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

     Screen plot displaying the plate configuration of a 'cellHTS'
     object.

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

     configurationAsScreenPlot(x, verbose=interactive(), posControls, negControls)

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

       x: a configured 'cellHTS' object (i.e. 'state(x)['configured']'
          must be 'TRUE').

 verbose: a logical value, if 'TRUE', the function reports some of its
          intermediate progress. The default is 'interactive()'.

posControls: a list or vector of regular expressions specifying the
          name of the positive controls. See details.

negControls: a vector of regular expressions specifying the name of the
          negative controls. See details.

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

     This function calls the function 'plotScreen' to create a screen
     plot showing the plate configuration (as defined by the plate
     configuration file used to configure the 'cellHTS' object - see
     function 'configure') used for the RNAi experiment stored in 'x'.

     'posControls' and 'negControls' should be given as vectors of
     regular expression patterns specifying the name(s) of the
     positive(s) and negative(s) controls, respectivey, as provided in
     the plate configuration file  (and acccessed via 'wellAnno(x)'). 

     By default, if 'posControls' is not given, "pos" will be taken as
     the annotation name for the wells containing positive controls.
     Similarly, if 'negControls' is missing, by default "neg" will be
     considered as the name used to annotate the negative controls. 
     The content of 'posControls' and 'negControls' will be passed to
     'regexpr' for pattern matching within the well annotation given in
     column 'controlStatus' of the 'featureData' slot of the 'cellHTS'
     object.

_V_a_l_u_e:

     Invisibly, a vector with the color map used to display the well
     annotation in the image plot.

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

     Ligia Bras ligia@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of
     cell-based RNAi screens, _Genome Biology_ *7*, R66.

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

     'plotScreen', 'writeReport'

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

         data("KcViab") 
         configurationAsScreenPlot(KcViab)

