controlDensity           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

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

     Plots the density of positive and negative controls (if
     applicable) for all controls contained in the dataset.

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

     controlDensity(header, dataset, channel, plotTitle, 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 

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:

     Plots the density of positive and negative controls (if
     applicable) for all controls contained in the dataset. The plot is
     saved as a pdf and a png file named after the experiment name
     specified in the header concatenated with the ' plotTitle'.

     The function returns the plot name.

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

     'controlDensityPerScreen', 'controlDensityPerPlate'

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

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

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

