plotProfile               package:GLAD               R Documentation

_P_l_o_t _g_e_n_o_m_i_c _p_r_o_f_i_l_e _a_n_d _c_y_t_o_g_e_n_e_t_i_c _b_a_n_d_i_n_g

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

     Plot genomic profile with breakpoints, outliers, smoothing line
     and cytogenetic banding.

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

     plotProfile.profileCGH(profileCGH, variable="LogRatio", Chromosome=NULL,
                            Smoothing=NULL, Bkp=FALSE,
                            labels=TRUE, plotband=TRUE, unit=0,
                            colDAGLAD=c("black","blue","red","green","yellow"),
                            colCytoBand=c("white","darkblue"),
                            colCentro="red", text=NULL, ...)

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

profileCGH: Object of class 'profileCGH'

variable: The variable to be plot.

Chromosome: A numeric vector with chromosome number to be plotted. Use
          23 and 24 for chromosome X and Y respectively. If 'NULL', all
          the genome is plotted.

Smoothing: The variable used to plot the smoothing line. If 'NULL',
          nothing is plotted.

     Bkp: If 'TRUE', the breakpoints are represented by a vertical red
          dashed line.

  labels: If 'TRUE', the labels of the cytogenetic banding are written.

plotband: If 'TRUE', the cytogenetic banding are plotted.

    unit: Give the unit of the PosBase. For example if 'unit=3',
          PosBase are in Kb, if 'unit=6', PosBase are in Mb, ...

colDAGLAD: Color code to plot Deletion, Amplification, Gain, Lost and
          Normal status.

colCytoBand: Color code for cytogenetic banding.

colCentro: Color code for centromere.

    text: A list with the parameters to be passed to the function
          'text'.

     ...: 

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

_V_a_l_u_e:

     A plot

_N_o_t_e:

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

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

     Philippe Hup, glad@curie.fr.

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

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

     ### Cytogenetic banding information
     data(cytoband)

     ###
     data(snijders)

     ### Creation of "profileCGH" object
     profileCGH <- as.profileCGH(gm13330)


     ###########################################################
     ###
     ###  glad function as described in Hup et al. (2004)
     ###
     ###########################################################

     res <- glad(profileCGH, mediancenter=FALSE,
                     smoothfunc="lawsglad", bandwidth=10, round=2,
                     model="Gaussian", lkern="Exponential", qlambda=0.999,
                     base=FALSE,
                     lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
                     type="tricubic", param=c(d=6),
                     alpha=0.001, msize=5,
                     method="centroid", nmax=8,
                     verbose=FALSE)

     ### Genomic profile on the whole genome
     plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing", plotband=FALSE)

     ### Genomic profile on the whole genome and cytogenetic banding
     plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing")

     ### Genomic profile for chromosome 1
     text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2)
     plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,
     Smoothing="Smoothing", plotband=FALSE, text=text)

     ### Genomic profile for chromosome 1 and cytogenetic banding with labels
     text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2)
     plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,
     Smoothing="Smoothing", text=text, main="Chromosome 1")

