heatmap                 package:aCGH                 R Documentation

_C_r_e_a_t_e_s _h_e_a_t_m_a_p _a_r_r_a_y _C_G_H _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Clusters samples and produces heatmapp of the observed log2ratios.

_U_s_a_g_e:

     heatmap(x, imp = TRUE, Rowv = NA, Colv = NULL, distfun = dist,
             hclustfun = hclust, add.expr, symm = FALSE,
             revC = identical(Colv, "Rowv"), scale = "none",
             na.rm = TRUE, margins = c(5, 5), ColSideColors,
             RowSideColors, cexRow = 0.2 + 1 / log10(nr),
             cexCol = 0.2 + 1 / log10(nc), labRow = NULL,
             labCol = NULL, main = NULL, xlab = NULL, ylab = NULL,
             verbose = getOption("verbose"), methodR = "ward",
             methodC = "ward", zlm = c(-0.5, 0.5), ...)

_A_r_g_u_m_e_n_t_s:

       x: object of the 'aCGH' object

     imp: logical variable indicating whether 'log2.ratios.imputed' or
          'log2.ratios' slot of 'aCGH' should be used. Defaults to
          imputed value (TRUE). 

    Rowv: determines if and how the row dendrogram should be computed
          and reordered.  Either a 'dendrogram' or a vector of values
          used to reorder the row dendrogram or 'NA' to suppress any
          row dendrogram (and reordering) or by default, 'NULL' 

    Colv: determines if and how the column dendrogram should be
          reordered.  Has the same options as the 'Rowv' argument above
          and additionally when 'x' is a square matrix, 'Colv = "Rowv"'
          means that columns should be treated identically to the rows. 

 distfun: function used to compute the distance (dissimilarity) between
          both rows and columns. Defaults to 'dist'.

hclustfun: function used to compute the hierarchical clustering when
          'Rowv' or 'Colv' are not dendrograms.  Defaults to 'hclust'

add.expr: expression that will be evaluated after the call to 'image'.
          Can be used to add components to the plot.

    symm: logical indicating if 'x' should be treated *symm*etrically;
          can only be true when 'x' is a square matrix.

    revC: logical indicating if the column order should be 'rev'ersed
          for plotting, such that e.g., for the symmetric case, the
          symmetry axis is as usual.

   scale: character indicating if the values should be centered and
          scaled in either the row direction or the column direction,
          or none.  The default is "row" if 'symm' false, and "none"
          otherwise.

   na.rm: logical indicating whether 'NA''s should be removed.

 margins: numeric vector of length 2 containing the margins (see
          'par(mar= *)') for column and row names, respectively.

ColSideColors: (optional) character vector of length 'ncol(x)'
          containing the color names for a horizontal side bar that may
          be used to annotate the columns of 'x'.

RowSideColors: (optional) character vector of length 'nrow(x)'
          containing the color names for a vertical side bar that may
          be used to annotate the rows of 'x'.

cexRow, cexCol: positive numbers, used as 'cex.axis' in for the row or
          column axis labeling.  The defaults currently only use number
          of rows or columns, respectively.

labRow, labCol: character vectors with row and column labels to use;
          these default to 'rownames(x)' or 'colnames(x)',
          respectively.

main, xlab, ylab: main, x- and y-axis titles;

 verbose: logical indicating if information should be printed.

 methodR: method to use for clustering rows. defaults to "ward"

 methodC: method to use for clustering columns. defaults to "ward"

     zlm: all the values greater or equal  than zlm are set to zlm -
          0.01. a;; value less or equal to -zlm are set to -zlm + 0.01 

     ...: additional arguments passed on to 'image', e.g., 'col'
          specifying the colors. 

_D_e_t_a_i_l_s:

     This function is almost identical to the 'heatmap' in base R. The
     slight modifications are that (1) a user can specify clustering
     method for rows and columns; (2) all the values outside specified
     limits are floored to be 0.01 less than a limit; (3) default
     values are different. Note that using default option of 'imp'
     (TRUE) produces nicer looking plots as all missing values are
     removed.

_V_a_l_u_e:

     Invisibly, a list with components 

 crowInd: row index permutation vector as returned by
          'order.dendrogram' 

  colInd: row index permutation vector as returned by
          'order.dendrogram' 

_R_e_f_e_r_e_n_c_e_s:

     heatmap function in base R

_S_e_e _A_l_s_o:

     'aCGH' 'clusterGenome'

_E_x_a_m_p_l_e_s:

     #default plotting method for the aCGH object
     data(colorectal)
     plot(colorectal)

     #to produce smoother looking heatmap, use imp = T: this will use imputed
     #slot of aCGH object

     plot(colorectal, imp = TRUE)

