imageScreen             package:cellHTS             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(x, ar = 3/5, zrange, map = FALSE, anno)

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

       x: a 'cellHTS' object that has already been scored (i.e.
          containing the slot 'score').

      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 'x$score'.

     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', 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 'x$score'.
          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  from the 'cellHTS' object 'x',
     'x$score'. When the annotation mapping is performed, by default,
     'anno' is set to: 

        1.  The content of 'x$geneAnno$GeneSymbol' (or
           'x$geneAnno$GeneID', if the former is not available), if 'x'
           is annotated;

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

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

     Ligia Braz ligia@ebi.ac.uk

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

         data(KcViabSmall) 
         x <- KcViabSmall   
         x <- normalizePlates(x, normalizationMethod="median", zscore="-")
         x <- summarizeReplicates(x) 
         imageScreen(x, zrange=c(-5,5))

