plotChip                package:HELP                R Documentation

_P_l_o_t _c_h_i_p _i_m_a_g_e

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

     Graphic display of spatially-linked data, particularly applicable
     for microarrays

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

     plotChip(x, y, z, ...)

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

       x: vector of numerical data determining x-coordinates of data on
          chip. 'x' can also handle 'ExpressionSet' (see
          'plotChip-methods' for more parameter details). 

       y: vector of numerical data determining y-coordinates of data on
          chip 

       z: the vector of numerical data to be plotted 

     ...: Arguments to be passed to methods (see 'plotChip-methods'):

     '_e_l_e_m_e_n_t' which element of 'AssayData' to use for a given
          'ExpressionSet' input (default is '"exprs"') 

     '_s_a_m_p_l_e' which element of 'sampleNames' to use as data (default is
          1). Can be a character matching a sample name or simply an
          integer indicating which sample to choose.

     '_f_e_a_t_u_r_e._x' which element of 'featureData' to use as X coordinate
          (default is '"X"'). Can be a character matching 'varLabel' or
          simply an integer indicating which feature to choose. 

     '_f_e_a_t_u_r_e._y' which element of 'featureData' to use as Y coordinate
          (default is '"Y"'). Can be a character matching 'varLabel' or
          simply an integer indicating which feature to choose. 

     '_n_a._r_m' logical; if 'TRUE', missing values are removed from 'x',
          'y', and 'z'. If 'FALSE' (default) any missing values cause
          an error. 

     '_m_a_i_n' an overall title for the plot: see 'title'. 

     '_x_l_a_b' a title for the x axis: see 'title'. 

     '_y_l_a_b' a title for the y axis: see 'title'. 

     '_c_o_l_o_r_s' vector of colors specifying the color scheme to use
          (default is 'rev(rainbow(n=20, start=0, end=1/3))'). Also
          determines the resolution of 'z' such that the more colors
          that are used allow finer discrimination of differences in
          'z'. 

     '_r_a_n_g_e' vector of numerical data of length 2 (default is 'c(NA,
          NA)') specifying range used to color-code data in 'z' 

     '_n_r_o_w_s' numerical input specifying the number of rows by which to
          divide the chip; default is 'NULL' which skips the division
          of data into blocks and results in individual spot resolution 

     '_n_c_o_l_s' numerical input specifying the number of columns by which
          to divide the chip; default is 'NULL' which skips the
          division of data into blocks and results in individual spot
          resolution 

     '...' other arguments to be passed to 'plot'. See 'plot'.  

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

     Reid F. Thompson (rthompso@aecom.yu.edu), Mark Reimers
     (mreimers@vcu.edu)

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

     'plotChip-methods'

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

     #demo(pipeline,package="HELP")

     x <- rep(1:100,100)
     y <- rep(1:100,each=100)
     z <- x*(1001:11000/1000)
     z <- z-mean(z)
     z <- z*(sample(1:10000/10000)+1)
     plotChip(x,y,z,main="Curved gradient",xlab="x",ylab="y")

     plotChip(x,y,sample(1:10000,size=10000),colors=gray(0:50/50),range=c(1,10000),main="Random noise")

     #rm(x,y,z)

