plotSpatialEffects          package:cellHTS          R Documentation

_P_l_a_t_e _p_l_o_t _w_i_t_h _t_h_e _r_o_w _a_n_d _c_o_l_u_m_n _o_f_f_s_e_t_s _e_s_t_i_m_a_t_e_d _b_y _t_h_e _B _s_c_o_r_e _m_e_t_h_o_d

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

     The function plots the per-plate row and column effects estimated
     by the B score method.

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

     plotSpatialEffects(x, whichChannel = 1, plateRange)

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

       x: a 'cellHTS' object that has already been normalized using the
          B score method (see details).

whichChannel: a numeric value giving the channel of 'x' to plot.

plateRange: a numeric vector giving the plate numbers to plot. If
          missing, the function considers all the plates.

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

     The function plots the plate plots displaying the row and column
     offsets (stored in slot 'rowcol.effects' of the 'cellHTS' object
     'x') within the plates in 'plateRange', and for channel
     'whichChannel', as determined by the B score method. Before
     plotting the spatial offsets, the values within the chosen channel
     ('whichChannel') are transformed in order to be confined in the
     range [-1, 1], as follows:


                 yt = (y - min(y))/(max(y) - min(y))


     Here, yt are the transformed values, and y the estimated spatial
     effects. The maximum and the minimum values are calculated using
     all the values in  'x$rowcol.effects[,,,whichChannel]'.

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

     Ligia Braz ligia@ebi.ac.uk

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

     'plotPlate', 'Bscore', 'normalizePlates', 'normalizeChannels'

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

         data(KcViabSmall)
         x = normalizePlates(KcViabSmall, normalizationMethod="Bscore", BscoreArgs=list(save.model = TRUE))
         ## see plate plots with the row and column estimated offsets for plates 1 and 3:
         plotSpatialEffects(x, plateRange=c(1,3))

