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

_U_s_a_g_e:

     riplot(object, title, xlab, ylab, 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'.

   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.

    xlab: The xlab for figures. The default figure xlab is 
          "expression(log[2](R*G))". One xlab would be used for all
          plot,  thus unlike title, user (if one wants) need to provide
          only one name.

    ylab: The ylab for figures. The default figure ylab is 
          "expression(log[2](R/G))". One ylab would be used for all
          plot,  thus unlike title, user (if one wants) need to provide
          only one name.

   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 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)
     ## End(Not run)

