displayTIFFImage          package:beadarray          R Documentation

_D_i_s_p_l_a_y _p_a_r_t _o_f _a _T_I_F_F _I_m_a_g_e

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

     Function for looking at a particular part of an image scanned from
     a BeadArray

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

     displayTIFFImage(BLData, array, a = 680:720, b = 680:720, flip=TRUE,
     showOutliers=TRUE, locateBeads=FALSE, showUnregistered=FALSE, outliers=NULL)

_A_r_g_u_m_e_n_t_s:

  BLData: an BeadLevelList object containing bead level data

   array: numeric value for the array that we want to look at

       a: vector giving the range of x values for the region we want to
          look at

       b: vector giving the range of y values for the region we want to
          look at 

    flip: if TRUE then the input y range of coordinates will be flipped
          so that y=0 will be at the top of the array

showOutliers: if TRUE then the location of outliers within the region
          will be highlighted on the plot

locateBeads: if TRUE then the plot will be interactive

showUnregistered: if TRUE then any unregistered points inside the
          region will be highlighted

outliers: List of BeadIDs which have been discovered to be outliers
          previously

_D_e_t_a_i_l_s:

     Loads up the original pgm image scanned from the array and
     displays the part of the image defined  by a and b. Intensities of
     pixels are given on the log2 scale with a brighter green
     indicating a value near 16.

     The 'showOutliers' parameter sets if outliers in the region are
     highlighted in the region with a default value of TRUE. All
     outliers which have intensity higher or lower than the mean for
     their bead type will  be displayed as blue or red dots
     respectively. Any beads which have negative intensity will be
     displayed as yellow dots.

     The 'showUnregistered' parameter allows beads which were not
     correctly decoded to be highlighted. Setting this parameter to
     TRUE causes any unregistered beads in the region to be displayed
     as grey dots.

     The 'flip' parameter arises from the fact that when we plot in R,
     we have the line y=0 at the \textit{bottom} of the plot, whereas
     on BeadArrays the y values are counted from the \textit{top} of
     the array. 

     Setting the locateBeads parameter to TRUE will make the plots
     produced interactive. In this mode, clicking on outliers on the
     image will display information about the unsharpened intensity, 
     the local background level along with the ProbeID for the bead and
     mean of all beads on the array with that ProbeID.

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

     Plot is produced on the current graphical device.

_A_u_t_h_o_r(_s):

     Mark Dunning and Isabelle Camilier

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

     data(BLData)

     ##The image files that are to be read need to be in the working directory

     ##displayTIFFImage(BLData, 1, a=1000:1400, b=1200:1400)

     ##To display unregistered beads

     ##displayTIFFImage(BLData, 1, a=1300:1600, b=400:600, showUnregistered=TRUE)

     ##To use plot interactively and find information about beads clicked on set 'locateBeads' parameter

     ##displayTIFFImage(BLData, 1, a=1300:1600, b=400:600, locateBeads=TRUE)

