channelPlot             package:RNAither             R Documentation

_P_l_o_t _s_i_g_n_a_l _c_h_a_n_n_e_l_s _a_g_a_i_n_s_t _e_a_c_h _o_t_h_e_r

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

     Generates plots allowing pairwise comparison of signal channels.
     Fits a lowess regression curve into the plots.

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

     channelPlot(header, dataset, vecOfChannels, flag, plotTitle, showPlot, smSpan=2/3)

_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' 

vecOfChannels: A vector containing the names of the signal channels to
          be compared, e.g. "SigIntensity" 

    flag: 0, 1, or 2. 0 uses the data from the complete dataset, 1
          makes comparisons for each experiment, 2 makes comparisons
          for each plate. 

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. 

  smSpan: The smoother span of the lowess curve. This gives the
          proportion of points in the plot which influence the smooth
          at each value. Larger values give more smoothness. Optional,
          defaults to 2/3

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

     Saves the plots in pdf and png files named after the experiment
     name specified in the header concatenated with the 'plotTitle',
     the number of the comparison, and if applicable the experiment
     number and/or the plate number.

     When 'flag' == 0, returns the plot name ('plotName'). 

     When 'flag' == 1, returns a list containing: 

plotName : The plot name 

minOfScreens: The number of the first experiment 

numOfScreens: The number of the last experiment 

     When 'flag' == 2, returns a list containing: the plot name, a
     vector with the number of the first experiment and of the last
     experiment, and a vector with the number of the first plate and
     the number of the last plate.

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")
     plotname <- channelPlot(header, dataset, c("SigIntensity", "NbCells"), 0, "Channel comparison", 1)

