plotDistributions         package:arrayMagic         R Documentation

_V_i_s_u_a_l_i_s_a_t_i_o_n _o_f _d_i_s_t_r_i_b_u_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Boxplot like visualisation of distributions, only the boxes, i.e.
     the median and the second and third quartile are plotted (cf.
     'boxplot.stats' for the details on the calculation). The plots may
     help to identify shortcomings of the raw data or normalised data.
     The argument 'quantiles' can be used to visualize two or three
     arbitrary quantiles with boxes.

_U_s_a_g_e:

     plotDistributions(dataMatrix, transFunc, quantiles, main, labels, xlab, ylab, colourVector, width=8, height=6, fileName="plotDistributionsOutput", savePath, plotOutput="standard", automaticSubtitle=TRUE)

_A_r_g_u_m_e_n_t_s:

dataMatrix: numeric data matrix, where columns represent distributions,
          e.g. raw array data or normalised data; required; default
          missing.

transFunc: unary function; optional; default missing. Data
          transformation function, e.g. log

quantiles: missing by default; a vector of two or three increasing
          quantiles used to determine the boxes to be drawn

    main: plot title; type character string; optional; default missing

  labels: vector of names, may substitute column names of 'dataMatrix';
          optional; default missing

    xlab: label for x axis; type character string; optional; default
          missing

    ylab: label for y axis; type character string; optional; default
          missing

colourVector: vector of colours; optional; default missing

   width: graphics window width; required; default: 8

  height: graphics window height; required; default: 6

fileName: optional; default: "plotDistributionsOutput"

savePath: optional; default: missing

plotOutput: character string specifying either "standard", "screen",
          "pdf", "win.metafile"; default: "standard"

automaticSubtitle: logical; required; default: 'TRUE'; The quantiles
          values are added as subtitle to the plot.

_D_e_t_a_i_l_s:

     Default of 'transFunc' is no transformation, i.e. identity. If
     'labels' are supplied at first the column names or secondly a
     numbering  are used instead. By default the 'colourVector' is
     defined as alternating "darkred" and "darkgreen". A data matrix
     which only consists of 'NA, NaN, Inf, -Inf' will cause a cryptical
     error.

_V_a_l_u_e:

     The function is called for its side effect.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'boxplot.stats'

_E_x_a_m_p_l_e_s:

           plotDistributions(cbind(rnorm(100),rnorm(100)),
                  main="Random Gaussians", labels = c("N1","N2"), ylab="scale")
           plotDistributions(as.matrix(1:100), quantiles=c(0.25,0.85),
                  main = "Random Gaussians", labels = c("N1"), ylab = "scale")
           plotDistributions(as.matrix(1:100), transFunc=log,
                  quantiles=c(0.1,0.95), main = "Random Gaussians",
                  labels = c("N1"), ylab = "scale")
                

