heatmap,pairwisefst-method {poolfstat}

Show pairwisefst object

Description

Show pairwisefst object

Usage

## S4 method for signature 'pairwisefst'
heatmap(
  x,
  Rowv = NULL,
  Colv = if (symm) "Rowv" else NULL,
  distfun = as.dist,
  hclustfun = hclust,
  reorderfun = function(d, w) reorder(d, w),
  add.expr,
  symm = FALSE,
  revC = identical(Colv, "Rowv"),
  scale = c("row", "column", "none"),
  na.rm = TRUE,
  margins = c(5, 5),
  ColSideColors,
  RowSideColors,
  cexRow = 0.2 + 1/log10(nrow(x@PairwiseFSTmatrix)),
  cexCol = 0.2 + 1/log10(ncol(x@PairwiseFSTmatrix)),
  labRow = NULL,
  labCol = NULL,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  keep.dendro = FALSE,
  verbose = getOption("verbose"),
  ...
)

Arguments

x

Object of class pairwisefst

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, see ‘Details’ below.

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 (and so if there is to be no row dendrogram there will not be a column one either).

distfun

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

hclustfun

function used to compute the hierarchical clustering when Rowv or Colv are not dendrograms. Defaults to hclust. Should take as argument a result of distfun and return an object to which as.dendrogram can be applied.

reorderfun

function(d, w) of dendrogram and weights for reordering the row and column dendrograms. The default uses reorder.dendrogram.

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 symmetrically; can only be true when x is a square matrix.

revC

logical indicating if the column order should be reversed 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; defaults to none.

keep.dendro

logical indicating if the dendrogram(s) should be kept as part of the result (when Rowv and/or Colv are not NA).

verbose

logical indicating if information should be printed.

...

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