LDheatmap             package:LDheatmap             R Documentation

_T_h_i_s _f_u_n_c_t_i_o_n _p_r_o_d_u_c_e_s _a _p_a_i_r_w_i_s_e _L_D _p_l_o_t

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

     "LDheatmap" is used to produce a graphical display, as a heat map,
     of linkage disequilibrium measures for SNPs. The heatmap is a
     false color image in the upper-left diagonal of a square plot.
     Optionally, a line parallel to the diagonal of the image
     indicating the physical or genetic map positions of the SNPs may
     be added, along with text reporting the total length of the
     genomic region considered.

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

     LDheatmap(gdat, map.distance = 1000*(1:ncol(gdat)), distances="physical",
     LDmeas = "r", title = NULL, add.map = TRUE, x.image.show = 0.2, 
     y.image.show = 0.2, line.position = 0.2, x.length.position = 0, 
     y.length.position = 0, SNP.name = NULL)

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

    gdat: SNP data: a data frame of genotype objects. 

map.distance: Vector of physical or genetic map distances, if known.
          Physical distances should be in bases, genetic distances
          should be in centiMorgans (cM). Default value is equispaced
          markers, 1000 bases apart. 

distances: A character string indicating whether distances are 
          "physical" or "genetic" distances. Default is "physical". If
          distances="physical", the text describing the total length of
          the region will be "Physical Length:XXkb" where XX is the
          length of the region in kilobases. If distances="genetic",
          the text will be "Genetic Map Length:YYcM" where YY is the
          length of the region in centiMorgans.

  LDmeas: A character value of LD measurement - either allelic
          correlation r^2 or Lewontin's |D'|; default = "r" for r^2;
          type "D'" for |D'|. 

   title: Character string for the title of the plot. Default = NULL
          will print out "Pairwise LD". 

 add.map: If TRUE, a diagonal line indicating the physical or genetic
          map positions of the SNPs will be added to the plot. 

x.image.show: A numeric value which will stretch the image window
          horizontally by the given amount; default = 0.2 will expand
          the plot area horizontally by 0.2 units to the right. 

y.image.show: A numeric value which will stretch the image window
          vertically by the given amount; default = 0.2 will expand the
          plot area vertically by 0.2 units downwards. 

line.position: Modifies the position of the line parallel to the
          diagonal of the matrix; the larger the value, the farther it
          lies from the matrix diagonal.

x.length.position: Modifies x-coordinate of the text labelling the
          total length of the genomic region being considered; e.g.,
          x.length.position=0.1 will move the text to the right by 0.1
          units from the original position in the upper right quadrant
          of the plot. 

y.length.position: Modifies y-coordinate of the text labelling the
          total length of the genomic region being considered; e.g.,
          y.length.position=0.1 will move the text upwards by 0.1 units
          from the original position in the upper right quadrant of the
          plot. 

SNP.name: A vector of character string(s) of SNP name(s) to be labelled
          in the plot. 

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

     The distance vector of SNP positions, if provided, is assumed to
     be in the same order as that of the SNPs in the data.

_W_a_r_n_i_n_g_s:

     It is not possible to draw multiple LDheatmap plots on a single
     graph area.

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

     Ji-hyung Shin <jshinb@sfu.ca>, Sigal Blay <sblay@sfu.ca>, Brad
     McNeney <mcneney@stat.sfu.ca>, Jinko Graham <jgraham@cs.sfu.ca>

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

     'LD', 'genotype', 'image'

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

      demo(LDheatmap) 

