genome.plot              package:MANOR              R Documentation

_P_a_n-_g_e_n_o_m_i_c _r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _a _n_o_r_m_a_l_i_z_e_d _a_r_r_a_y_C_G_H

_D_e_s_c_r_i_p_t_i_o_n:

     Displays a pan-genomic representation of a normalized arrayCGH.

_U_s_a_g_e:

       ## S3 method for class 'arrayCGH':
       genome.plot(arrayCGH, x="PosOrder", y="LogRatio",
         chrLim=NULL, col.var=NULL, clim=NULL, cex=NULL, pch=NULL, ...)  
       ## Default S3 method:
       genome.plot(data, pch=NULL, cex=NULL, xlab="", ylab="", ...)

_A_r_g_u_m_e_n_t_s:

arrayCGH: an object of type 'arrayCGH'

    data: a data frame with two columns: 'x' and 'y', and optionally a
          column data$chrLim giving the limits of each chromosome

       x: a variable name from 'arrayCGH\$cloneValues' giving the order
          position of the clones along the genome (defaults to
          'PosOrder')

       y: a variable name from 'arrayCGH\$cloneValues' to be plotted
          along the genome (defaults to 'LogRatio')

  chrLim: an optional variable name from 'arrayCGH\$cloneValues' giving
          the limits of each chromosome

 col.var: a variable name from 'arrayCGH\$cloneValues' defining the
          color legend

    clim: a numeric vector of length 2: color range limits (used if
          'col.var' is numeric)

     cex: a numerical value giving the amount by which plotting text
          and symbols should be scaled relative to the default: see
          'par'

    xlab: a title for the x axis: see 'title'

    ylab: a title for the y axis: see 'title'

     pch: either an integer specifying a symbol or a single character
          to be used as the default in plotting points: see 'par' 

     ...: further arguments to be passed to 'plot'

_D_e_t_a_i_l_s:

     if 'col.var' is a numeric variable, 'y' colors are proportionnal
     to 'col.var' values; if it is a character variable or a factor,
     one color is assigned to each different value of 'col.var'. If
     'col.var' is NULL, colors are proportionnal to 'y' values.

_N_o_t_e:

     People interested in tools for array-CGH analysis can visit our
     web-page: <URL: http://bioinfo.curie.fr>.

_A_u_t_h_o_r(_s):

     Pierre Neuvial, manor@curie.fr.

_S_e_e _A_l_s_o:

     'flag', 'report.plot'

_E_x_a_m_p_l_e_s:

     data(spatial)

     ## default color code: log-ratios
     ## Not run: 
     genome.plot(edge.norm, chrLim="LimitChr")
     ## End(Not run)

     ## color code determined by a qualitative variable: ZoneGNL (DNA copy number code)
     edge.norm$cloneValues$ZoneGNL <- as.factor(edge.norm$cloneValues$ZoneGNL)
     ## Not run: 
     genome.plot(edge.norm, col.var="ZoneGNL")
     ## End(Not run)
     ## comparing profiles with and without normalization
     ## aggregate data without normalization (flags)

     gradient.nonorm <- norm.arrayCGH(gradient, flag.list=NULL, var="LogRatio",
     FUN=median, na.rm=TRUE)
     gradient.nonorm <- sort.arrayCGH(gradient.nonorm)

     ## Not run: 
     genome.plot(gradient.nonorm, pch=20, main="Genomic profile without
     normalization", chrLim="LimitChr")   
     x11()
     genome.plot(gradient.norm, pch=20, main="Genomic profile with
     normalization", chrLim="LimitChr")   
     ## End(Not run)

