parallelCoordinates         package:biclust         R Documentation

_P_a_r_a_l_l_e_l _C_o_o_r_d_i_n_a_t_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Represents expression levels through gene and/or condition
     profiles in a bicluster as lines.

_U_s_a_g_e:

     parallelCoordinates(x, bicResult, number,plotBoth=FALSE, plotcol=TRUE, compare=TRUE,info=F,bothlab=c("Rows","Columns"),ylab="Value",col=1,...)

_A_r_g_u_m_e_n_t_s:

       x: The data matrix of the bicluster to be drawn

bicResult: BiclustResult object with a bicluster result set

  number: Bicluster to be drawn from the result set 'bicResult'

plotBoth: If 'TRUE', Parallel Coordinates of rows (Genes) and columns
          (Conditions) were drawn one below the other.

 plotcol: If 'TRUE', columns profiles are drawn, so each line
          represents one of the columns in the bicluster. Otherwise,
          row profiles are drawn. Default 'TRUE'

 compare: If 'TRUE',  values of the complete data matrix are considered
          and drawn as shaded lines. Default 'TRUE'

    info: If 'TRUE', a prepared Title is drawn

 bothlab: Names of the X-Axis if PlotBoth

    ylab: ylab

     col: col

     ...: Plot Parameters

_A_u_t_h_o_r(_s):

     Rodrigo Santamaria and Sebastian Kaiser rodri@usal.es

_S_e_e _A_l_s_o:

     'drawHeatmap' for alternative representation of biclusters and
     'bubbleplot' for simultaneous representation of biclusters.

_E_x_a_m_p_l_e_s:

       #Random 100x50 matrix with a single, up-regulated 10x10 bicluster
       s2=matrix(rnorm(5000),100,50)
       s2[11:20,11:20]=rnorm(100,3,0.3)
       set.seed(1)
       bics <- biclust(s2,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
       iter.startup = 5, iter.layer = 30,  verbose = TRUE)
       parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=TRUE, plotcol=TRUE, compare=TRUE, info=TRUE,bothlab=c("Genes Bicluster 1","Conditions Bicluster 1"))
       parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=FALSE, plotcol=TRUE,  compare=FALSE, info=TRUE)

