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)

