plot.LD             package:GeneticsBase             R Documentation

_T_e_x_t_u_a_l _a_n_d _g_r_a_p_h_i_c_a_l _d_i_s_p_l_a_y _o_f _l_i_n_k_a_g_e _d_i_s_e_q_u_i_l_i_b_r_i_u_m (_L_D) _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Textual and graphical display of linkage disequilibrium (LD)
     objects

_U_s_a_g_e:

     plot(x, y, ...)
     plot.LD (x, y=NULL, cex, ...)
     LDView(LdMat,
            SNPloc=NULL,
            is.triangle=TRUE,
            SNPnames=NULL,
            cexSNPnames=0.2+1/log10(nrow(LdMat)),
            margins=c(6,2,3,6),
            main=NULL,
            barCol=rainbow(256,start=0,end=1/6 ),
            widths=c(10,10),
            heights=c(1,10),
            ...)

_A_r_g_u_m_e_n_t_s:

       x: LD or LDband object

       y: currently ignored

     cex: Scaling factor for table text. If absent, text will be scaled
          to fit within the table cells.

   LdMat: matrix of pair-wise LD measures

  SNPloc: SNP locations

is.triangle: indicate if 'LdMat' is a lower triangle matrix or not. if
          'LdMat' is an upper triangle, then the user has to transpose
          it before calling the function 'LDView'.

SNPnames: labels for SNPs

cexSNPnames: font size for SNPs labels

 margins: margins for heatmap

    main: title for the plot

  barCol: specify the color scheme

  widths: The plot is split into two parts - upper part and lower part
          'widths' specifies the widths of the two parts

 heights: The plot is split into two parts - upper part and lower part
          'heights' specifies the heights of the two parts

     ...: Optional arguments ('plot.LD.data.frame' passes these to
          'LDtable' and 'LDplot') and other parameters for the function
          'image'

_D_e_t_a_i_l_s:

     LDtable generates a graphical matrix of LD coefficients.  It
     attempts to properly set the font size so that the estimated
     values fit into the boxes.  It also colorized the boxes to whether
     the estimates are significantly different from no linkage.

     LDplot generates a plot of the LD coeffients across markers.  By
     default it will overlay plots for LD against all markers.  LD
     against a specific subset of markers can be obtained using the
     'marker' argument.

_V_a_l_u_e:

SNPnames: labels of the SNPs in 'LDView'

   LdMat: LD matrix

  SNPloc: SNP positions

_A_u_t_h_o_r(_s):

     Gregory R. Warnes warnes@bst.rochester.edu

_S_e_e _A_l_s_o:

     'LD', 'geneSet', 'diseq'

_E_x_a_m_p_l_e_s:

     # load the data
     data(CAMP)

     # compute pairwise LD
     ld <- LD(CAMP)

     print(ld)    # text display of LD coefficents and graphical display of LD estimates

     LDView(t(ld@"R^2"), SNPloc=1:8, SNPnames=CAMP@markerInfo$Name)

     ## LDtable(ld) # graphical display of LD estimates
     ## LDtable(ld, which="D'", digits=2) # graphical display of D' only 

     ## plot(CAMP) # two panel display

