plotSpatialEffects         package:cellHTS2         R Documentation

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_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 or by the spatial normalization.

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

     plotSpatialEffects(object, channel = 1, plates)

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

  object: a 'cellHTS' object that has been normalized using the B score
          method or other spatial normalization (see details).

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

  plates: a vector of integers giving the plate numbers to plot. If
          missing, the function considers all of 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)
     within the plates in 'plates', and for channel 'channel', as
     determined by the 'B score method' or 'spatial normalization'.
     Before plotting the spatial offsets, the values within the chosen
     channel (argument 'channel') are transformed in order to be
     confined in the range [0, 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  'plateEffects(object)$rowcol[,,channel]'.

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

     Ligia P. Bras ligia@ebi.ac.uk

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

     'plotPlate', 'Bscore', 'spatialNormalization', 'normalizePlates',
     'summarizeChannels'

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

         data(KcViabSmall)
         x <- normalizePlates(KcViabSmall, scale="multiplicative", log=TRUE, method="Bscore", save.model = TRUE)
         ## see plate plots with the row and column estimated offsets for plates 1 and 3:
         plotSpatialEffects(x, plates=c(1,3))

