plotChr             package:geneplotter             R Documentation

_P_l_o_t _S_m_o_o_t_h_e_d _S_e_n_s_e/_A_n_t_i-_s_e_n_s_e _o_f _S_p_e_c_i_f_i_e_d _C_h_r_o_m_o_s_o_m_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     For a given chromosome, plot the smooths of the sense and the 
     anti-sense from 5' to 3' (left to right on x-axis).

_U_s_a_g_e:

     plotChr(chrN, senseObj, cols = rep("black", length(senseObj[[1]])), log = FALSE, xloc = c("equispaced", "physical"), geneSymbols = FALSE, ngenes = 20, lines.at = NULL, lines.col = "red")

_A_r_g_u_m_e_n_t_s:

    chrN: The desired chromosome, e.g. for humans it would be a
          character string in the set of c(1:22, "X", "Y").

senseObj: The result of 'Makesense'.

    cols: A vector of colors for the lines in the plot, typically
          specified according to a certain pheotype of samples.

     log: Logical, whether log-transformation should be taken on the
          smoothed expressions.

    xloc: Determines whether the "Representative Genes"  will be
          displayed according to their relative  positions on the
          chromosome (physical), or spaced  evenly (equispaced). 
          Default is equispaced.

geneSymbols: Logical, whether to use Affy IDs or  Gene Symbols for
          "Representative Genes", default is  Affy IDs.

  ngenes: Desired number of "Representative Genes". The  number of
          actual displayed genes may differ.

lines.at: A vector of Affy IDs. Vertical lines will  be drawn at
          specified genes.

lines.col: A vector of colors associated with  'lines.at'.

_A_u_t_h_o_r(_s):

     Robert Gentleman and Xiaochun Li

_S_e_e _A_l_s_o:

     'Makesense'

_E_x_a_m_p_l_e_s:

     example(Makesense)

     op <- par(ask=TRUE)

     cols <- ifelse(expressionSet133a$cov1=="test 1", "red", "green")
     plotChr("21", esetobj, cols)

     # plot on log-scale:

     plotChr("21", esetobj, cols, log=TRUE)

     # genesymbol instead of probe names:

     plotChr("21", esetobj, cols, log=TRUE, geneSymbols=TRUE)

     # add vertical lines at genes of interest:

     gs <- c("220372_at", "35776_at", "200943_at")
     plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs)

     # add vertical lines at genes of interest
     # with specified colors:

     gs <- c("220372_at", "35776_at", "200943_at")
     cc <- c("blue", "cyan","magenta")
     plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs,
     lines.col=cc)
     par(op)