loadingplot             package:adegenet             R Documentation

_R_e_p_r_e_s_e_n_t_s _a _c_l_o_u_d _o_f _p_o_i_n_t_s _w_i_t_h _c_o_l_o_r_s

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

     The 'loadingplot' function represents positive values of a vector
     and identifies the values above a given threshold. It can also
     indicate groups of observations provided as a factor. 

     Such graphics can be used, for instance, to assess the weight of
     each variable (loadings) in a given analysis.

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

     loadingplot(x, at=NULL, threshold=quantile(x,0.75), axis=1, fac=NULL, byfac=FALSE,
                 lab=names(x), cex.lab=0.7, cex.fac=1, lab.jitter=0,
                 main="Loading plot", xlab="Variables", ylab="Loadings",...)

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

       x: either a vector with numeric values to be plotted, or a
          matrix-like object containing numeric values. In such case,
          the 'x[,axis]' is used as vector of values to be plotted.

      at: an optional numeric vector giving the abscissa at which
          loadings are plotted. Useful when variates are SNPs with a
          known position in an alignement.

threshold: a threshold value above which values of x are identified. By
          default, this is the third quartile of x.

    axis: an integer indicating the column of x to be plotted; used
          only if x is a matrix-like object.

     fac: a factor defining groups of observations.

   byfac: a logical stating whether loadings should be averaged by
          groups of observations, as defined by 'fac'.

     lab: a character vector giving the labels used to annotate values
          above the threshold.

 cex.lab: a numeric value indicating the size of annotations.

 cex.fac: a numeric value indicating the size of annotations for groups
          of observations.

lab.jitter: a numeric value indicating the factor of randomisation for
          the position of annotations. Set to 0 (by default) implies no
          randomisation.

    main: the main title of the figure.

    xlab: the title of the x axis.

    ylab: the title of the y axis.

     ...: further arguments to be passed to the plot function.

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

     Invisibly returns a list with the following components:
      - threshold: the threshold used
      - var.names: the names of observations above the threshold
      - var.idx: the indices of observations above the threshold
      - var.values: the values above the threshold

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

     Thibaut Jombart t.jombart@imperial.ac.uk

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

     x <- runif(20)
     names(x) <- letters[1:20]
     grp <- factor(paste("group", rep(1:4,each=5)))

     ## basic plot
     loadingplot(x)

     ## adding groups
     loadingplot(x,fac=grp,main="My title",cex.lab=1)

