controlDensityPerScreen       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 _e_x_p_e_r_i_m_e_n_t

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

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

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

     controlDensityPerScreen(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:

     Generates a series of plots for each experiment, 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'
     and the number of the experiment.

     The function returns a list of length 3 containing:

plotName : the plotname 

minOfScreens : the number of the first experiment 

numOfScreens : the number of the last experiment 

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

     'controlDensity', 'controlDensityPerPlate'

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

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

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

