plotSnp               package:SNPchip               R Documentation

_P_l_o_t_s _c_o_p_y _n_u_m_b_e_r _a_n_d _g_e_n_o_t_y_p_e _c_a_l_l_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Plots copy number and genotype call versus physical position for
     an arbitrary number of samples and chromosomes.

_U_s_a_g_e:

     plotSnp(object, chromosomes, samples, snpId = c(NA, 1e+06), oma = c(5, 4, 4, 0.5), mar = c(0.5, 0, 0.5, 0.2), width.right = NULL, showLayout = FALSE, plot = TRUE, col = c("royalblue", "red", "royalblue", "green3"), bg = rep("white", 4), cex = c(2, 3, 2, 2), pch = rep(".", 4), col.centromere = c("bisque", NA), bw = FALSE, lwd = 2, col.axis = "brown", cex.axis = 1, cex.main = 1, cex.lab = 1, xlim = NULL, ylim = NULL, log = "", xaxis.side = rep(c(1, 3), length.out = length(chromosomes)), xaxs = "i", xaxt = "n", yaxs = "i", yaxt = "n", xlab = "", ylab = "", lab = c(2, 5, 7), adj = 0, main = "", legend = c(TRUE, TRUE), legend.panel = c(TRUE, FALSE), legend.location = c("topright", "bottomright"), legend.bty = c("n", "n"), legend.col = c("white", "white"), ncol = 2, cex.legend = c(1, 1), digits = 3, pt.cex = cex.legend * 1.5, bty = "n", addCytoband = FALSE, height.cytoband = 0.5, ...)

_A_r_g_u_m_e_n_t_s:

  object: Object of class 'AnnotatedSnpCopyNumberSet' or
          'AnnotatedSnpSet'

chromosomes: Vector of character strings for chromosome number.
          Chromosomes will be plotted in the order given.

 samples: Vector of integers indicating sample number.

   snpId: Not yet implemented.

     oma: See 'par'

     mar: See 'par'

width.right: Width of panel for the legend relative to the width of the
          smallest chromosome.

showLayout: Logical for whether to display the output of 'layout' for
          plotting

    plot: Logical.  If FALSE, only the output from 'layout' is
          displayed.

     col: A character or numerical vector indicating the color to plot
          genotype call:  AA color, AB color,  BB color, no call color.
           For 'AnnotatedSnpCopyNumberSet', only the first color is
          used.

      bg: A character or numerical vector indicating the background
          color for the plotting symbols.  Possible to specify a
          different background for each genotype call in the same order
          as 'col'.

     cex: A numerical vector of plotting symbol size in the same order
          as 'col'.

     pch: A character or numerical vector of plotting symbol size in
          the same order as 'col'.

col.centromere: Vector of length two: color of centromere and color for
          the centromere border. 

      bw: Converts all colors to grayscale.  

     lwd: See 'par'

col.axis: See 'par'

cex.axis: See 'par'

cex.main: See 'par'

 cex.lab: See 'par'

    xlim: See 'par'

    ylim: See 'par'

     log: See 'par'

xaxis.side: Vector of integers indicating whether to plot the x-axis on
          the top (3) or bottom (1) for each sample.  The default is to
          alternate top/bottom.

    xaxs: See 'par'

    xaxt: See 'par'

    yaxs: See 'par'

    yaxt: See 'par'

    xlab: See 'par'

    ylab: See 'par'

     lab: See 'par'

     adj: See 'par'

    main: See 'par'

  legend: Logical vector of length 2.  If both are TRUE, a legend for
          descriptive statistics (legend 1) and plotting symbols
          (legend 2) are generated.

legend.panel: Logical vector of length 2.  Whether to draw the legends
          on a separate panel.

legend.location: Character vector of length 2.  Where to draw the
          legends. See 'legend'.

legend.bty: Character vector of length 2.  See the argument 'bty' in
          function 'legend'.

legend.col: Character vector of length 2. See the argument 'bty' in
          function 'legend'. 

    ncol: Number of columns in legend for plotting symbols.  See
          'legend'.

cex.legend: Same as argument 'cex' in function 'legend'.

  digits: Rounds values in legend to the number of digits specified.

  pt.cex: See 'legend'

     bty: See 'par'

addCytoband: Logical indicating whether to add a cytoband.

height.cytoband: Height of cytoband relative to height of samples.

     ...: Additional arguments

_D_e_t_a_i_l_s:

_V_a_l_u_e:

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Robert Scharpf

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

     'par', 'plot', 'legend'

_E_x_a_m_p_l_e_s:

     data(annSnpset)
     plotSnp(annSnpset, chromosomes=c(1:22, "X"), 
             samples=1:4, width.right=10, cex.axis=1, lab=c(3, 3, 5),
             cex.lab=1.2, cex.legend=c(1, 1.2))

