plot                 package:KCsmart                 R Documentation

_P_l_o_t _a _s_a_m_p_l_e _p_o_i_n_t _m_a_t_r_i_x

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

     Plot the sample point matrix or parts of it

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

     plot(x,y, ...)
     ## S4 method for signature 'scaleSpace, missing':
     plot(x, y, spm, type='b', ...)
     ## S4 method for signature 'samplePointMatrix, missing':
     plot(x, y, type="b", sigLevels=NULL, chromosomes=NULL, colinAxis=NULL, fillColor=NULL, maploc=NULL, interpolation=1, main=NULL, col=NULL, ylim=NULL, add=F, ...)
     ## S4 method for signature 'compKc, missing':
     plot(x, sigRegions=NULL, type="1", chromosomes=NULL, colinAxis=NULL, maploc=NULL, interpolation=1, main=NULL, col1=NULL, col2=NULL, ylim=NULL, add=F, ...)

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

       x: either an object of class samplePointMatrix, scaleSpace or
          compKc

       y: object of class missing

    type: Determines which data is plotted. 'g' for gains only, 'l' for
          losses only and 'b' and '1' for both in one plot device

     spm: add stuff here

sigRegions: The significant regions as calculated by the
          compKcSigRegions function

sigLevels: If given, the cutoffs will be drawn as lines in the plots.
          Optional 

chromosomes: Takes a vector of chromosomes to be plotted. Defaults to
          all chromosomes. 

colinAxis: Allows you to override default behaviour of axis labeling.
          Choose False for genomic position labeling for each
          individual chromosome, True for colinear labeling.

fillColor: Allows you to choose the colors used to fill the significant
          areas under the curve. Takes a list with the 'pos' element
          giving the color for the gains and the 'neg' element the
          color for the losses. 

  maploc: Currently not in use

interpolation: Determines which points from the sample point matrix
          will actually be plotted. If the value of 'interpolation' is
          n, then every n-th point will be plotted. The default value
          of 1 will results in all points being plotted. This can be
          useful when a high density sample point matrix results in big
          file size when exporting the image (especially to pdf or eps
          format).

    main: Set the title of the plot

     col: Set the color of the plotted lines

    col1: Set the color of the plotted lines

    col2: Set the color of the plotted lines

    ylim: Set the y-axis limits

     add: When set to true the plot is added to the current plot device

     ...: Any other parameters you would like to pass to 'plot'. See
          'par' for more details.

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

     Plots the sample point matrix. The gains and the losses are
     plotted separately. The KC normalized score is plotted on the
     y-axis, the genomic position on the x-axis. If centromeres are
     present these are represented by dotted, lightblue lines. Setting
     type to 'b' or to '1' will both make the plot appear in one plot
     device, '1' will plot the gains and the losses in one plot, 'b'
     will plot the gains and losses separately. Using the 'add' flag it
     is possible to add a plot to the current plot device. The 'col'
     and 'ylim' arguments can be used to set the color of each plot and
     the plot regions. The function 'idPoints' can be used to identify
     points in the sample point matrix plot. See the corresponding
     documentation for details.

     In case of plotting a compKc object, col1 and col2 can be used to
     set the colors of the group 1 and group 2 mean values
     respectively.

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

     Jorma de Ronde

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

     'calcSpm', 'plotScaleSpace', 'idPoints'

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

     data(hsSampleData)
     data(hsMirrorLocs)

     spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

     plot(spm1mb)
     plot(spm1mb, interpolation=10)
     plot(spm1mb, chromosomes=c(1,4,'X'))

     siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)
     plot(spm1mb, chromosomes=c(1,4,'X'), sigLevels=siglevel1mb)
     plot(spm1mb, chromosomes=c(1,4,'X'), sigLevels=siglevel1mb, fillColor=list(pos='darkred',neg='darkgreen'))

