multiecdf            package:geneplotter            R Documentation

_M_u_l_t_i_p_l_e _e_m_p_i_r_i_c_a_l _c_u_m_u_l_a_t_i_v_e _d_i_s_t_r_i_b_u_t_i_o_n _f_u_n_c_t_i_o_n_s (_e_c_d_f) _a_n_d _d_e_n_s_i_t_i_e_s

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

     Plot multiple empirical cumulative distribution functions (ecdf)
     and densities with user interface similar to that of 'boxplot'.

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

     multiecdf(x, ...)
     ## S3 method for class 'formula':
     multiecdf(formula, data = NULL, xlab, na.action = NULL, ...)
     ## S3 method for class 'matrix':
     multiecdf(x, xlab, ...) 
     ## S3 method for class 'list':
     multiecdf(x,
               xlim,
               col = brewer.pal(9, "Set1"),
               main = "ecdf",
               xlab,
               do.points = FALSE,
               subsample = 1000L,
               legend = list(
                 x = "right",
                 legend = if(is.null(names(x))) paste(seq(along=x)) else names(x),
                 fill = col),
               ...)

     multidensity(x, ...)
     ## S3 method for class 'formula':
     multidensity(formula, data = NULL, xlab, na.action = NULL, ...)
     ## S3 method for class 'matrix':
     multidensity(x, xlab, ...) 
     ## S3 method for class 'list':
     multidensity(x,
                  bw = "nrd0",
                  xlim,
                  ylim,
                  col  = brewer.pal(9, "Set1"),
                  main = if(length(x)==1) "density" else "densities",
                  xlab,
                  lty  = 1L,
                  legend = list(
                    x = "topright",
                    legend = if(is.null(names(x))) paste(seq(along=x)) else names(x),
                    fill = col),
                  ...)

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

 formula: a formula, such as 'y ~ grp', where 'y' is a numeric vector
          of data values to be split into groups according to the
          grouping variable 'grp' (usually a factor).

    data: a data.frame (or list) from which the variables in 'formula'
          should be taken.

na.action: a function which indicates what should happen when the data
          contain 'NA's.  The default is to ignore missing values in
          either the response or the group.

       x: a list of numeric vectors.

      bw: the smoothing bandwidth, see the manual page for 'density'.
          If 'bw' is a character string specifying a rule to choose the
          bandwidth, this rule is applied to 'x[[1]]' and then the same
          numerical value of 'bw' is used throughout.

    xlim: Range of the x axis. If missing, the data range is used.

    ylim: Range of the y axis. If missing, the range of the density
          estimates is used.

col, lty: Line colors and line type.

    main: Plot title.

    xlab: x-axis label.

do.points: logical; if 'TRUE', also draw points at the knot locations.

subsample: numeric or logical of length 1. If numeric, and larger than
          0, subsamples of that size are used to compute and plot the
          ecdf for those elements of 'x' with more than that number of
          observations. If logical and 'TRUE', a value of 1000 is used
          for the subsample size.

  legend: a list of arguments that is passed to the function 'legend'.

     ...: Further arguments that get passed on to the 'plot' functions.

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

     The usefulness of 'multidensity' can vary, depending on the data
     and because of smoothing artifacts. 'multiecdf' will in many cases
     be preferable.

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

     For the 'multidensity' functions, a list of 'density' objects.

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

     Wolfgang Huber <URL: http://www.ebi.ac.uk/huber>

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

     'boxplot', 'ecdf', 'density'

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

       words = strsplit(packageDescription("geneplotter")$Description, " ")[[1]]
       factr = factor(sample(words, 2000, replace = TRUE))
       x = rnorm(length(factr), mean=as.integer(factr))
       
       multiecdf(x ~ factr)
       multidensity(x ~ factr)

