heatmap.2: Enhanced Heat Map (from gplots)

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Enhanced Heat Map (from gplots)

Description

A heat map is a false color image (basically image(t(x))) with a dendrogram added to the left side and/or to the top. Typically, reordering of the rows and columns according to some set of values (row or column means) within the restrictions imposed by the dendrogram is carried out. This heatmap provides a number of extensions to the standard R heatmap function.

Usage

heatmap.2(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
  distfun = dist, hclustfun = hclust, dendrogram = c("both", "row",
  "column", "none"), reorderfun = function(d, w) reorder(d, w),
  symm = FALSE, scale = c("none", "row", "column"), na.rm = TRUE,
  revC = identical(Colv, "Rowv"), add.expr, breaks, symbreaks = any(x <
  0, na.rm = TRUE) || scale != "none", col = "heat.colors", colsep,
  rowsep, sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote,
  notecex = 1, notecol = "cyan", na.color = par("bg"),
  trace = c("column", "row", "both", "none"), tracecol = "cyan",
  hline = median(breaks), vline = median(breaks), linecol = tracecol,
  margins = c(5, 5), ColSideColors, RowSideColors, cexRow = 0.2 +
  1/log10(nr), cexCol = 0.2 + 1/log10(nc), labRow = NULL,
  labCol = NULL, srtRow = NULL, srtCol = NULL, adjRow = c(0, NA),
  adjCol = c(NA, 0), offsetRow = 0.5, offsetCol = 0.5,
  colRow = NULL, colCol = NULL, key = TRUE, keysize = 1.5,
  density.info = c("histogram", "density", "none"), denscol = tracecol,
  symkey = any(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
  key.title = NULL, key.xlab = NULL, key.ylab = NULL,
  key.xtickfun = NULL, key.ytickfun = NULL, key.par = list(),
  main = NULL, xlab = NULL, ylab = NULL, lmat = NULL,
  lhei = NULL, lwid = NULL, extrafun = NULL, ...)

Arguments

x	numeric matrix of the values to be plotted.
Rowv	determines if and how the row dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and no reordering is done. If a dendrogram, then it is used "as-is", ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector.
Colv	determines if and how the column dendrogram should be reordered. Has the 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.
dendrogram	character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured.
reorderfun	function(d, w) of dendrogram and weights for reordering the row and column dendrograms. The default uses statsreorder.dendrogram
symm	logical indicating if x should be treated symmetrically; can only be true when x is a square matrix.
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 "none".
na.rm	logical indicating whether NA's should be removed.
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.
add.expr	expression that will be evaluated after the call to image. Can be used to add components to the plot.
breaks	(optional) Either a numeric vector indicating the splitting points for binning x into colors, or a integer number of break points to be used, in which case the break points will be spaced equally between min(x) and max(x).
symbreaks	Boolean indicating whether breaks should be made symmetric about 0. Defaults to TRUE if the data includes negative values, and to FALSE otherwise.
col	colors used for the image. Defaults to heat colors (heat.colors).
colsep	(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color sepcolor.
rowsep	(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color sepcolor.
sepcolor	(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color sepcolor.
sepwidth	(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box drawn by colsep and rowsep as a function of the width (colsep) or height (rowsep) of a cell. Defaults to c(0.05, 0.05)
cellnote	(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols.
notecex	(optional) numeric scaling factor for cellnote items.
notecol	(optional) character string specifying the color for cellnote text. Defaults to "cyan". Can be a matrix to personalise each cell.
na.color	Color to use for missing value (NA). Defaults to the plot background color.
trace	character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'column'.
tracecol	character string giving the color for "trace" line. Defaults to "cyan".
hline	Vector of values within cells where a horizontal or vertical dotted line should be drawn. The color of the line is controlled by linecol. Horizontal lines are only plotted if trace is 'row' or 'both'. Vertical lines are only drawn if trace 'column' or 'both'. hline and vline default to the median of the breaks, linecol defaults to the value of tracecol.
vline	Vector of values within cells where a horizontal or vertical dotted line should be drawn. The color of the line is controlled by linecol. Horizontal lines are only plotted if trace is 'row' or 'both'. Vertical lines are only drawn if trace 'column' or 'both'. hline and vline default to the median of the breaks, linecol defaults to the value of tracecol.
linecol	Vector of values within cells where a horizontal or vertical dotted line should be drawn. The color of the line is controlled by linecol. Horizontal lines are only plotted if trace is 'row' or 'both'. Vertical lines are only drawn if trace 'column' or 'both'. hline and vline default to the median of the breaks, linecol defaults to the value of tracecol.
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	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.
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	character vectors with row and column labels to use; these default to rownames(x) or colnames(x), respectively.
labCol	character vectors with row and column labels to use; these default to rownames(x) or colnames(x), respectively.
srtRow	angle of row/column labels, in degrees from horizontal
srtCol	angle of row/column labels, in degrees from horizontal
adjRow	2-element vector giving the (left-right, top-bottom) justification of row/column labels (relative to the text orientation).
adjCol	2-element vector giving the (left-right, top-bottom) justification of row/column labels (relative to the text orientation).
offsetRow	Number of character-width spaces to place between row/column labels and the edge of the plotting region.
offsetCol	Number of character-width spaces to place between row/column labels and the edge of the plotting region.
colRow	color of row/column labels, either a scalar to set the color of all labels the same, or a vector providing the colors of each label item
colCol	color of row/column labels, either a scalar to set the color of all labels the same, or a vector providing the colors of each label item
key	logical indicating whether a color-key should be shown.
keysize	numeric value indicating the size of the key
density.info	character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key.
denscol	character string giving the color for the density display specified by density.info, defaults to the same value as tracecol.
symkey	Boolean indicating whether the color key should be made symmetric about 0. Defaults to TRUE if the data includes negative values, and to FALSE otherwise.
densadj	Numeric scaling value for tuning the kernel width when a density plot is drawn on the color key. (See the adjust parameter for the density function for details.) Defaults to 0.25.
key.title	main title of the color key. If set to NA no title will be plotted.
key.xlab	x axis label of the color key. If set to NA no label will be plotted.
key.ylab	y axis label of the color key. If set to NA no label will be plotted.
key.xtickfun	function computing tick location and labels for the xaxis of the color key. Returns a named list containing parameters that can be passed to axis. See examples.
key.ytickfun	function computing tick location and labels for the y axis of the color key. Returns a named list containing parameters that can be passed to axis. See examples.
key.par	graphical parameters for the color key. Named list that can be passed to par.
main	main, x- and y-axis titles; defaults to none.
xlab	main, x- and y-axis titles; defaults to none.
ylab	main, x- and y-axis titles; defaults to none.
lmat	visual layout: position matrix, column height, column width. See below for details
lhei	visual layout: position matrix, column height, column width. See below for details
lwid	visual layout: position matrix, column height, column width. See below for details
extrafun	A function to be called after all other work. See examples.
...	additional arguments passed on to image

Value

invisibly, a list with components rowInd row index permutation vector as returned by order.dendrogram. colInd column index permutation vector. call the matched call rowMeans, rowSDs mean and standard deviation of each row: only present if scale="row" colMeans, colSDs mean and standard deviation of each column: only present if scale="column" carpet reordered and scaled 'x' values used generate the main 'carpet' rowDendrogram row dendrogram, if present colDendrogram column dendrogram, if present breaks values used for color break points col colors used vline center-line value used for column trace, present only if trace="both" or trace="column" hline center-line value used for row trace, present only if trace="both" or trace="row" colorTable A three-column data frame providing the lower and upper bound and color for each bin layout A named list containing the values used for lmat, lhei, and lwid.

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.