plotPairs                package:HELP                R Documentation

_P_l_o_t _t_r_e_e-_p_a_i_r_s

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

     Pairwise comparison of samples producing a matrix of scatterplots
     and a corresponding dendrogram

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

     plotPairs(x, ...)

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

       x: a numeric matrix, where each column represents a different
          sample. 'x' can also be of class '"ExpressionSet"'. 

     ...: Arguments to be passed to methods (see 'plotPairs-methods'):

          '_e_l_e_m_e_n_t' which element of 'AssayData' to use for a given
               'ExpressionSet' input (default is '"exprs"') 

          '_s_a_m_p_l_e_s' which samples to use as data. Can be a vector of
               characters matching sample names, integers indicating
               which samples to choose, or a mixture of the two. If
               'NULL' (default), all samples will be used.

          '_s_c_a_l_e' logical value indicating whether sample branch
               lengths should be scaled by distance (default is 'TRUE') 

          '_g_r_o_u_p_s' logical value indicating whether the samples should
               be organized and color-coded by group (default is
               'TRUE') 

          '_d_i_s_t._m_e_t_h_o_d' the distance measure to be used. This must be
               one of '"euclidean"' (default), '"maximum"',
               '"manhattan"', '"canberra"', '"binary"' or
               '"minkowski"'. Any unambiguous substring can be given:
               see 'dist' for more details. 

          '_h_c_l_u_s_t._m_e_t_h_o_d' the agglomeration method to be used. This
               should be (an unambiguous abbreviation of) one of
               '"ward"' (default), '"single"', '"complete"',
               '"average"', '"mcquitty"', '"median"' or '"centroid"':
               see 'hclust' for more details. 

          '_k' an integer scalar or vector with the desired number of
               groups. If 'NULL' (default), grouping will rely instead
               on distance measurements: see 'cutree' for more details. 

          '...' other arguments to be passed to 'pairs' or 'dist'. See
               'pairs', 'dist'.

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

     Reid F. Thompson (rthompso@aecom.yu.edu)

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

     'plotPairs-methods', 'dist', 'hclust', 'dendrogram', 'cutree',
     'pairs'

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

     #demo(pipeline,package="HELP")

     x <- sample(1:10000,size=10000)
     x <- cbind(x,x+5,x*sample((1000:2000)/1000,size=10000,replace=TRUE),sample(-1*(1:10000),size=10000))
     colnames(x) <- c("x","x+5","spread","random")
     plotPairs(x)

     #rm(x)

