ZScorePlot             package:RNAither             R Documentation

_P_l_o_t _n_o_r_m_a_l_i_z_e_d _i_n_t_e_n_s_i_t_y _v_a_l_u_e_s _p_e_r _w_e_l_l

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

     Plots the normalized intensity values for each well, together with
     a black line showing the mean, two green lines showing the
     standard deviation, and two red lines showing 2 standard
     deviations.

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

     ZScorePlot(header, dataset, flag, col4plot, col4anno, plotTitle, 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' 

    flag: either 1 or 2. 1 if the dataset contains values per well, 2
          if the dataset contains summarized values for each siRNA
          (e.g. a dataset summarized with 'summarizeReps'). 

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

col4anno: a character string specifying the column that will be used
          for the plot annotation 

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. 

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

     Plots the normalized intensity values for each well, together with
     a black line showing the mean, and two red lines showing 2
     standard deviations. Clicking on the points shows the gene/siRNA
     name.

     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:

     'plotBar', 'ZScorePlotTwo'

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

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

     normedvals <- ZScore(header, dataset, list("SigIntensity", 1))
     ZScorePlot(normedvals[[1]], normedvals[[2]], 1, "SigIntensity", "GeneName",
     "Normed intensity values per well", 1)

