graph1D                package:made4                R Documentation

_P_l_o_t _1_D _g_r_a_p_h _o_f _a_x_i_s _f_r_o_m _m_u_l_t_i_v_a_r_i_a_t_e _a_n_a_l_y_s_i_s

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

     Draw 1D plot of an axis from multivariate analysis. Useful for
     visualising an individual axis from  analyses such as PCA
     'dudi.pca' or COA 'dudi.coa'.  It accepts a factor so that groups
     of points can be coloured. It can also be used for graphing genes,
     and will only label n genes at the ends of the axis.

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

     graph1D(dfx,  classvec=NULL,ax = 1, hor=FALSE, s.nam=row.names(dfx), n=NULL,
            scaled=TRUE, col="red", width=NULL, ...)

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

     dfx: 'vector', 'matrix', or 'data.frame', which contains a column 
          with axis coordinates

      ax: Numeric, indicating column of 'matrix', or 'data.frame' to be
          plotted.  The default is 1.

classvec: Factor, indicating sub-groupings or classes in dfx or
          dfx[,ax]

     hor: Logical, indicating whether the graph should be drawn
          horizontal or vertically.  The default is vertically.

   s.nam: Vector. labels of dfx, The default is row.names(dfx)

       n: Numeric. Whether all rows should be plotted, n=10 would label
          only the 10 variables at the end of the axis.  By default all
          variables (row of dfx) are labelled

  scaled: 

     col: A character or vector indicating the colour(s) for points or
          groups of points. If points are to be coloured according to a
          factor, length(col) should equal length(levels(classvec))

   width: A vector of length 2, which is the width (of a vertical plot)
          or height (of a  horizontal plot). This can be increased if
          variable labels are unreadable. The default is c(-2,1)

     ...: further arguments passed to or from other methods 

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

     Aedin Culhane

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

     'between.graph'

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

     a<-rnorm(25)
     graph1D(a, s.nam=letters[1:25])
     graph1D(a, s.nam=letters[1:25], col="blue", pch=19,  n=3)
     data(khan)
     if (require(ade4, quiet = TRUE)) {
     khan.coa<-dudi.coa(khan$train, scan=FALSE, nf=2)
     }
     graph1D(khan.coa$co, ax=1)

