plotErrorBars              package:puma              R Documentation

_P_l_o_t _m_e_a_n _e_x_p_r_e_s_s_i_o_n _l_e_v_e_l_s _a_n_d _e_r_r_o_r _b_a_r_s _f_o_r _o_n_e _o_r _m_o_r_e _p_r_o_b_e_s_e_t_s

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

     This produces plots of probesets of interest.

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

     plotErrorBars(
             eset
     ,       probesets = if(dim(exprs(eset))[1] <= 12) 1:dim(exprs(eset))[1] else 1
     ,       arrays = 1:dim(pData(eset))[1] # default is to use all
     ,       xlab = paste(colnames(pData(eset))[1:numOfFactorsToUse(eset)], collapse=":")
     ,       ylab = "Expression Estimate"
     ,       xLabels = apply(
                       as.matrix(pData(eset)[arrays,1:numOfFactorsToUse(eset)])
                     , 1
                     , function(mat){paste(mat, collapse=":")}
                     )
     ,       ylim = NA
     ,       numOfSEs = qnorm(0.975)
     ,       globalYlim = FALSE # Not yet implemented!
     ,       plot_cols = NA
     ,       plot_rows = NA
     ,       featureNames = NA
     ,       showGeneNames = TRUE
     ,       showErrorBars = if(
                                             length(assayDataElement(eset,"se.exprs"))==0 ||
                                             length(assayDataElement(eset,"se.exprs")) == sum(is.na(assayDataElement(eset,"se.exprs")))
                                             ) FALSE else TRUE
     ,       plotColours = FALSE
     ,       log.it = if(max(exprs(eset)) > 32) TRUE else FALSE
     ,       eset_comb = NULL
     ,       jitterWidth = NA
     ,       qtpcrData = NULL
     , ...
     )

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

    eset: An object of class 'ExpressionSet'. This is the main object
          being plotted. 

probesets: A vector of integers indicating the probesets to be plotted.
          These integers refer to the row numbers of the 'eset'. 

  arrays: A vector of integers indicating the arrays to be shown on
          plots. 

    xlab: Character string of title to appear on x-axis 

    ylab: Character string of title to appear on y-axis 

 xLabels: Vector of strings for labels of individual points on x-axis. 

    ylim: 2-element numeric vector showing minimum and maximum values
          for y-axis. 

numOfSEs: Numeric indicating the scaling for the error bars. The
          default value give error bars that include 95% of expected
          values. 

globalYlim: Not yet implemented! 

plot_cols: Integer specifying number of columns for multi-figure plot. 

plot_rows: Integer specifying number of rows for multi-figure plot. 

featureNames: A vector of strings for 'featureNames' (Affy IDs). This
          is an alternative (to the 'probesets' argument) way of
          specifying probe sets. 

showGeneNames: Boolean indicating whether to use Affy IDs as titles for
          each plot. 

showErrorBars: Boolean indicating whether error bars should be shown on
          plots. 

plotColours: A vector of colours to plot. 

  log.it: Boolean indicating whether expression values should be
          logged. 

eset_comb: An object of class 'ExpressionSet'. This is a secondary
          object to be plotted on the same charts as 'eset'. This
          should be an object created using 'pumaComb' which holds the
          values created by combining information from the replicates
          of each condition. 

jitterWidth: Numeric indicating the x-axis distance between replicates
          of the same condition. 

qtpcrData: A 2-column matrix of qRT-PCR values (or other data to be
          plotted on the same charts). 

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

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

     This function has no return value. The output is the plot created.

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

     Richard D. Pearson

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

             #       Next 4 lines commented out to save time in package checks, and saved version used
         # if (require(affydata)) {
             #       data(Dilution)
             #       eset_mmgmos <- mmgmos(Dilution)
             # }
             data(eset_mmgmos)
             plotErrorBars(eset_mmgmos)
             plotErrorBars(eset_mmgmos,1:6)

