image.RGList              package:Ringo              R Documentation

_F_u_n_c_t_i_o_n _t_o _v_i_s_u_a_l_i_z_e _s_p_a_t_i_a_l _d_i_s_t_r_i_b_u_t_i_o_n _o_f _r_a_w _i_n_t_e_n_s_i_t_i_e_s

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

     Function to visualize spatial distribution of raw intensities on
     NimbleGen Oligoarrays. Requires 'RGList' with component 'genes'
     complete with 'genes$X' and 'genes$X' coordinates of probes on
     array. 'arrayImage' is a synonym of 'image.RGList'.

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

     ## S3 method for class 'RGList':
     image(x,arrayno,channel=c("red","green","logratio"),
              mycols=NULL, mybreaks=NULL,...)

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

       x: object of class 'RGList' containing red and green channel raw
          intensities; possibly result of 'readNimblegen'.

 arrayno: integer; which array to plot; one of '1:ncol(x$R)'

 channel: character; which channel to plot, either 'red', 'green' or
          the 'logratio' 'log2(red)-log2(green)'

  mycols: vector of colors to use for image; if 'NULL' defaults to
          'colorRampPalette(c("White", "Yellow", "Red"))(10)'

mybreaks: optional numeric vector of breaks to use as argument 'breaks'
          in 'image.default'; default 'NULL' means take
          'length(mycols)+1' quantiles of the data as breaks.

     ...: further arguments passed on to 'image.default'

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

     invisibly returns matrix of raw intensities, in which rows and
     columns correspond to X and Y coordinates on arrays. Can be
     directly plotted with function 'image.default'.

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

     Joern Toedling toedling@ebi.ac.uk

_S_e_e _A_l_s_o:

     'readNimblegen','image'

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

        exDir <- system.file("exData",package="Ringo")
        exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
        image(exRG,arrayno=1,channel="red")
        ## this example looks strange because the example data files only
        ## includes the probe intensities of probes mapped to the forward
        ## strand of chromosome 9.
        ## you can see these probes are distributed all over the array

