boxplot                package:oligo                R Documentation

_B_o_x_p_l_o_t

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

     Boxplot for observed (log-)intensities in a FeatureSet-like object
     (ExpressionFeatureSet, ExonFeatureSet, SnpFeatureSet,
     TilingFeatureSet).

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

     boxplot(x, ...)
     ## S4 method for signature 'FeatureSet':
     boxplot(x, which=pmindex(x), transfo=log2,
     range=0, ...)
     ## S4 method for signature 'ExpressionSet':
     boxplot(x, which=1:nrow(x), transfo=identity,
     range=0, ...)

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

       x: a 'FeatureSet'-like object or 'ExpressionSet' object.

   which: an integer vector determining which rows of 'x' should be
          plotted. See 'Details'.

 transfo: a function to transform the data before plotting. See
          'Details'.

   range: this determines how far the plot whiskers extend out from the
          box.  If 'range' is positive, the whiskers extend to the most
          extreme data point which is no more than 'range' times the
          interquartile range from the box. A value of zero causes the
          whiskers to extend to the data extremes.

     ...: arguments to be passed to plot

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

     The 'which' argument should be used to subset the object to be
     plotted. For example, if the user wants to plot the PM probes, he
     should use 'which=pmindex(x)', if MM probes are to be plotted
     'which=mmindex(x)'. If all probes are to be plotted
     'which=1:nrow(x)'. Note that pmindex/mmindex options will not work
     for summarized data.

     The 'transfo' argument will set the transformation to be used. For
     raw data, 'transfo=log2' is a common practice. For summarized data
     (which are often in log2-scale), no transformation is needed
     (therefore 'transfo=identity').

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

     'hist', 'image'

