riplot                package:maanova                R Documentation

_R_a_t_i_o _i_n_t_e_n_s_i_t_y _p_l_o_t _f_o_r _2-_d_y_e _M_i_c_r_o _A_r_r_a_y _e_x_p_e_r_i_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function only works for 2-dye array at this time. It will
     plot the log-ratio (log2(R/G)) versus log-intensity (log2(R*G)/2)
     figure for Micro Array experiment. Ideal RI plot will be points
     scattered around the y=0 horizontal line.

     This function works for both 'rawdata' and 'madata'.  This
     function and 'arrayview' assume the data field in 'rawdata' is on
     the raw scale, and in 'madata' is on log2 based scale. So if your
     rawdata is pre-transformed, you should not do riplot on the raw
     data.

_U_s_a_g_e:

     riplot(object, title, array, color = "blue", highlight.flag = TRUE, 
         flag.color = "Red", idx.highlight, highlight.color = "Green", 
         rep.connect = FALSE, onScreen=TRUE) 

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'madata' or 'rawdata'.

   title: The title for figures. The default figure title is "RI plot
          for array number X". If the user wants to provide titles, be
          sure to provide a string array with the same number of
          elements as the number of arrays.

   array: A list of arrays numbers for which you want to draw an RI
          plot.

   color: The color for the points in scatter plot. Default is blue.

highlight.flag: A logical parameter to indicate whether to highlight
          the bad spots or not.

flag.color: The color for bad spots, default is red.

idx.highlight: A vector for highlighted spots other than bad spots.

highlight.color: The color for highlighted spots. Default is green.

rep.connect: A logical value to represent whether to connect the dots
          between the replicates or not.

onScreen: A logical value to represent whether to display the plots on
          screen or not. If TRUE, x11() (in Unix/Windows) or
          macintosh() (in Mac) will be called inside the function.
          Otherwise, it will plot the figure on the current device.
          Default is TRUE.

_N_o_t_e:

     This function will plot one figure for each array. So if you have
     many arrays, there will be many figures generated.

_A_u_t_h_o_r(_s):

     Hao Wu

_E_x_a_m_p_l_e_s:

     ## Not run: 
     data(kidney)
     ############################
     # riplot on rawdata
     ############################
     # riplot raw data on screen
     riplot(kidney.raw)
     graphics.off()
     # riplot raw data array 1 and 3 and output to postscript file
     postscript(file="kidneyRIplot.ps")
     riplot(kidney.raw, array=c(1,3), onScreen=FALSE)

     ############################
     # RI plot on madata
     ############################
     data1 <- createData(kidney.raw)
     # do RI plot for all arrays
     riplot(data1)
     graphics.off()
     ## End(Not run)

