controlDensityPerPlate       package:RNAither       R Documentation

_P_l_o_t_t_i_n_g _t_h_e _c_o_n_t_r_o_l _d_e_n_s_i_t_y _p_e_r _p_l_a_t_e

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

     Plots the density of positive and negative controls (if
     applicable) for each plate.

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

     controlDensityPerPlate(header, dataset, channel, plotTitle, plotDesign, showPlot, supHisto)

_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' 

 channel: a character string specifying the name of the column
          containing the values for computing the density, e.g.
          '"SigIntensity"' 

plotTitle: the plot title 

plotDesign: 1 or 2. 1 will generate one window containing all plots, 2
          will generate a series of plots 

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 

supHisto: 0 or 1. 1 will additionally superimpose a colour histogram of
          the values for the positive and negative controls. Otherwise
          choose 0.

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

     Generates a series of plots for each experiment and each plate,
     showing the density of positive and negative controls (if
     applicable). The plots are saved as pdf and png files named after
     the experiment name specified in the header concatenated with the
     ' plotTitle'.

     The function returns a list of length 3 containing: 

plotName : the plot name 

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:

     'controlDensity', 'controlDensityPerScreen'

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

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

     controlDensityPerPlate(header, dataset, "SigIntensity", "Control density", 1, 1, 1)

