heatmap.3: Heatmap function

In pneuvial/c3co: Cancer Cell Clonality using Copy-Number

Description

Heatmap function

Usage

heatmap.3(x, 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 = max(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", "column", "row", "both"),
  tracecol = "cyan", hline = median(breaks), vline = median(breaks),
  linecol = tracecol, margins = c(5, 5), ColSideColors, RowSideColors,
  side.height.fraction = 0.3, cexRow = 0.2 + 1/log10(nr),
  cexCol = 0.2 + 1/log10(nc), cexMain = 1.5, cexKey = 1,
  cexColorKey = 1, labRow = NULL, labCol = NULL, key = TRUE,
  keysize = 1.5, density.info = c("none", "histogram", "density"),
  denscol = tracecol, symkey = max(x < 0, na.rm = TRUE) || symbreaks,
  densadj = 0.25, main = NULL, xlab = NULL, ylab = NULL,
  lmat = NULL, lhei = NULL, lwid = NULL, ColSideColorsSize = 1,
  RowSideColorsSize = 1, KeyValueName = "", ...)

Arguments

x,	matrix
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,	expression that will be evaluated after the call to image. Can be used to add components to the plot.
breaks,	numeric, 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 range(x). DEFAULT: 16 when not specified.
symbreaks	= max(x < 0, na.rm = TRUE) || scale != "none",
col	= "heat.colors",
colsep,	color for columns of separation.
rowsep,	color for lines of separation.
sepcolor	= "white",
sepwidth	= c(0.05, 0.05),
cellnote,	optional) matrix of character strings which will be placed within each color cell, e.g. cell labels or p-value symbols.
notecex	= 1,
notecol	= "cyan",
na.color	= par("bg"),
trace	= c("none", "column","row", "both"),
tracecol	= "cyan",
hline	= median(breaks),
vline	= median(breaks),
linecol	= tracecol,
margins	= c(5,5),
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 horizontal side bar that may be used to annotate the rows of x.
side.height.fraction	= 0.3, the width-to-height ratio of the heatmap.
cexRow	= 0.2 + 1/log10(nr),
cexCol	= 0.2 + 1/log10(nc),
cexMain	= 1.5, size of main
cexKey	= 1, size of name of key
cexColorKey	= 1, ## size of key
labRow	= NULL,
labCol	= NULL,
key	= TRUE,
keysize	= 1.5,
density.info	= c("none", "histogram", "density"),
denscol	= tracecol,
symkey	= max(x < 0, na.rm = TRUE) || symbreaks,
densadj	= 0.25,
main	= NULL,
xlab	= NULL,
ylab	= NULL,
lmat	= NULL,
lhei	= NULL,
lwid	= NULL,
ColSideColorsSize	= 1,
RowSideColorsSize	= 1,
KeyValueName	= "", name of key
...	additional parameters of graphics::image().

Value

A Heatmap

pneuvial/c3co documentation built on May 25, 2019, 10:21 a.m.