Usage
heatmap.3(x, max_score=6, Rowv = TRUE,
Colv = if (symm) "Rowv" else TRUE,
distfun = dist, hclustfun = hclust,
dendrogram = c("both", "row", "column", "none"),
symm = FALSE, scale = c("none", "row", "column"),
na.rm = TRUE, revC = identical(Colv,"Rowv"),
add.expr, breaks,
symbreaks = min(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("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, key = TRUE, keysize = 1.5,
density.info = c("histogram", "density", "none"),
denscol = tracecol,
symkey = min(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
main = NULL, xlab = NULL, ylab = NULL, lmat = NULL,
lhei = NULL, lwid = NULL,
leftMargin = 7, bottomMargin = 7, reverse = FALSE, ...)Arguments
x
numeric matrix of the TROM scores (-log$_{10}$ transformed Bonferroni corrected p-values) to be plotted.
max_score
numeric value specifying the saturated value of TROM scores, i.e., -log$_{10}$ (transformed Bonferroni corrected p-values). The TROM scores are saturated at max_score: TROM score=min(TROM score, max_score). The defualt v
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 reorderin 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
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. Should take as argument a result of distfun and return an object to which as.dendrogram can be applied.
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 honored.
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 from lower left to upper right.
add.expr
expression that will be evaluated after the call to image. Can be used to add components to the plot, eg., add.expr=abline(...)
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, rowsep, sepcolor
(optional) vector of integers indicating which columns or rows, should be separated from the preceding columns or rows by a box of the color sepcolor.
sepwidth
(optional) vector of length 2 giving the line width of the 2 vertical lines and the line width of the 2 horizontal lines of the separation box to be drawn, as a proportion of the width or height of a cell. Defaults to c(0.05, 0.05)
cellnote
(optional) matrix of character strings which will be placed inside some cells, e.g. p-value symbols.
notecex
(optional) numeric scaling factor for cellnote. Defaults to 1.
notecol
(optional) character string specifying the color for cellnote. Defaults to "cyan".
na.color
color to use for missing value (NA). Defaults to the background color.
trace
character string indicating whether a solid "trace" line should be drawn along "row"s or down "column"s, "both" or "none". The distance of the line from the center of each colored 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,vline,linecol
(optional) 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 is "
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. Defaults to 0.2 + 1/log$_{10}$(nr) and 0.2 + 1/log$_{10}$(ncol), respectively.
labRow, labCol
character vectors with row and column labels to use. Defaults to rownames(x) and colnames(x), respectively.
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.
main, xlab, ylab
main, x- and y-axis titles; defaults to "".
lmat, lhei, lwid
visual layout: position matrix, column height, column width.
leftMargin, bottomMargin
sets the left and bottom margins respectively of the plot region.
reverse
Boolean indicating whether to reverse the rows of x.
...
additional arguments passed on to image.