imageScreen             package:cellHTS2             R Documentation

_E_x_p_e_r_i_m_e_n_t-_w_i_d_e _q_u_a_l_i_t_y _c_o_n_t_r_o_l _p_l_o_t _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:

     Experiment-wide quality control plot of a scored 'cellHTS' object.

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

     imageScreen(object, ar = 3/5, zrange, map = FALSE, anno)

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

  object: a 'cellHTS' object that has already been scored (i.e.
          'state(object)['scored']=TRUE').

      ar: the desired aspect ration for the image plot (i.e. number of
          columns per number of rows)

  zrange: the range of values to be mapped into the color scale. If
          missing, 'zrange' will be set to the range of the score
          values stored in slot 'assayData' of 'object'.

     map: a logical value that determines whether an image map should
          be created using tooltips to indicate the annotation at each
          position. It only makes sense to set it to 'TRUE' when the
          function is called from 'writeReport' function, so the
          default is 'FALSE'.

    anno: optional input giving the annotation information for the
          mapping. It should be a vector of the same size as the total
          number of featured in 'object'. See details.

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

     This function creates an image plot that gives an overview of the
     whole set of score values stored in slot 'assayData' of a scored
     'cellHTS' object. When the annotation mapping is performed, by
     default, 'anno' is set to: 

        1.  (if 'object' is annotated) The content of column named
           'GeneSymbol' or named 'GeneID' (if the former is not
           available) of the 'featureData' slot of 'object';

        2.  The position within the plate, if 'object' is not
           annotated.

_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:

     'normalizePlates', 'summarizeChannels', 'scoreReplicates',
     'summarizeReplicates', 'Data' 'writeReport'

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

         data(KcViabSmall) 
         x <- KcViabSmall   
         x <- normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
         x <- scoreReplicates(x, sign="-", method="zscore") 
         x <- summarizeReplicates(x, summary="min") 
         imageScreen(x, zrange=c(-5,5))

