plotGenome               package:aCGH               R Documentation

_P_l_o_t_s _t_h_e _g_e_n_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     Basic plot of the log2 ratios for each array ordered along the
     genome.

_U_s_a_g_e:

     plotGenome(aCGH.obj, samples = 1:num.samples(aCGH.obj), naut = 22,
                Y = TRUE, X = TRUE, data = log2.ratios(aCGH.obj),
                chrominfo = human.chrom.info.Jul03,
                yScale = c(-2, 2), samplenames = sample.names(aCGH.obj),
                ylb = "Log2Ratio")

_A_r_g_u_m_e_n_t_s:

aCGH.obj: an object of class aCGH

 samples: vector containing indeces of the samples to be plotted.

    naut: number of autosomes in the organism

       Y: TRUE if chromosome Y is to be plotted, FALSE otherwise

       X: TRUE if chromosome X is to be plotted, FALSE otherwise

    data: a matrix containing values to use for plotting. defaults to
          the 'log2.ratios(aCGH.obj)'.

chrominfo: a chromosomal information associated with the mapping of the
          data.

  yScale: Minimum y-scale to use for plotting. Scale is expanded if any
          of the values exceed the positive or negative limit. 

samplenames: sample names.

     ylb: label for the Y-axis.

_S_e_e _A_l_s_o:

     'aCGH'

_E_x_a_m_p_l_e_s:

     #plot samples in the order of descending quality 
     data(colorectal)
     order.quality <- order(sd.samples(colorectal)$madGenome)
     pdf("plotGenome.orderByQuality.pdf")
     par(mfrow=c(2,1))
     for(i in order.quality)
        plotGenome(colorectal, samples = i, Y = FALSE)
     dev.off()

