spatialDistrib           package:RNAither           R Documentation

_G_e_n_e_r_a_t_e _s_p_a_t_i_a_l _p_l_o_t_s _o_f _i_n_t_e_n_s_i_t_y _v_a_l_u_e_s

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

     Generate plots of plates and their intensity values.

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

     spatialDistrib(header, dataset, plotTitle, col4plot, col4anno, showPlot)

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

  header: the header of a dataset file generated with
          'generateDatasetFile' 

 dataset: an R data frame generated with 'generateDatasetFile' 

plotTitle: the plot title 

col4plot: a character string specifying the column whose values will be
          used for the plot 

col4anno: a character string specifying the column whose values will be
          used for the annotation of the plot 

showPlot: 0 or 1. 1 will open one or several plot windows in the R GUI,
          0 will only save the plot(s) without opening windows. 

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

     For each plate, the plot will be saved as a png file named after
     the experiment name specified in the header concatenated with the
     ' plotTitle', the number of the experiment, and the number of the
     plate.

     Wells containing positive controls are marked with a "P", wells
     containing negative controls with an "N".

     Each plate will also be saved as an html file containing
     mouse-overs with the siRNA name for each well.

     The function returns a list containing:

histoName : the plotname

c(minOfScreens, numOfScreens) : a vector with the number of the first
          experiment and of the last experiment

c(minOfPlates, numOfPlates) : a vector with the number of the first
          plate and the number of the last plate

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

     'compareReplicateSD', 'compareReplicateSDPerScreen'

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")

     spatialDistrib(header, dataset, "Spatial distribution of cell counts", "NbCells", "GeneName", 1)

