Heatmap with Phylogeny Structured Columns

This function uses the heatmap function to plot the (normalized) data, using the phylogenetic tree as the column dendogram.

Usage

phyHeatmap(
  object,
  design = NULL,
  coef = NULL,
  phy,
  scale = "none",
  ColSideColors = NULL,
  add.expr = NULL,
  ...
)

Arguments

object: a matrix data object containing normalized expression values, with rows corresponding to genes and columns to samples (species).
design: the design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated. Defaults to the unit vector (intercept).
coef: column number or column name specifying which coefficient or contrast of the linear model in the design matrix is of interest. If left NULL, defaults to the last column of design.
phy: an object of class phylo, representing the phylogenetic relationships between the species. It must be dated and ultrametric. If the column names of object follow the pattern SpeciesName_SampleId or SpeciesName.SampleId, an automatic matching of the samples on the tip of the tree is performed. Otherwise, the tree tip labels must match with species names in col_species (see below). The tip labels of the tree can also match exactly the names as the columns of object, so that the tree directly includes all the replicates.
scale: character indicating if the values on the heatmap should be centered and scaled in either the row direction or the column direction, or none. The default is "none", as the data is assumed to be already normalized. This scaling only affects the colour scale; it does not scale the original data. See documentation of heatmap.
ColSideColors: (optional) character vector of length ncol(object) containing the color names for a horizontal side bar that may be used to annotate the columns of the heatmap. If left NULL and design is specified, the column of the design matrix corresponding to coef will be used.
add.expr: expression that will be evaluated after the call to image. Can be used to add components to the plot. See documentation of heatmap. If left NULL and design is specified, the column of the design matrix corresponding to coef will be used to draw vertical lines.
...: further arguments to be passed to heatmap. Argument Colv defaults to the phylogeny, and cannot be overwritten.

Value

Invisibly, a list, see heatmap.