heatmap.3: a minor change to heatmap.2 makes heatmap.3

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

a minor change to heatmap.2 makes heatmap.3

Description

heatmap.2 is the devil.

Usage

heatmap.3(
  x,
  Rowv = TRUE,
  Colv = if (symm) "Rowv" else TRUE,
  distfun = dist,
  hclustfun = fastcluster::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 = 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("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,
  key = TRUE,
  keysize = 1.5,
  density.info = c("histogram", "density", "none"),
  denscol = tracecol,
  symkey = min(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,
  linewidth = 1,
  ...
)

Arguments

x	data
Rowv	add rows?
Colv	add columns?
distfun	distance function to use
hclustfun	clustering function to use
dendrogram	which axes to put trees on
reorderfun	reorder the rows/columns?
symm	symmetrical?
scale	add the scale?
na.rm	remove nas from the data?
revC	reverse the columns?
add.expr	no clue
breaks	also no clue
symbreaks	still no clue
col	colors!
colsep	column separator
rowsep	row separator
sepcolor	color to put between columns/rows
sepwidth	how much to separate
cellnote	mur?
notecex	size of the notes
notecol	color of the notes
na.color	a parameter call to bg
trace	do a trace for rows/columns?
tracecol	color of the trace
hline	the hline
vline	the vline
linecol	the line color
margins	margins are good
ColSideColors	colors for the columns as annotation
RowSideColors	colors for the rows as annotation
cexRow	row size
cexCol	column size
labRow	hmmmm
labCol	still dont know
srtRow	srt the row?
srtCol	srt the column?
adjRow	adj the row?
adjCol	adj the column?
offsetRow	how far to place the text from the row
offsetCol	how far to place the text from the column
key	add a key?
keysize	if so, how big?
density.info	for the key, what information to add
denscol	tracecol hmm ok
symkey	I like keys
densadj	adj the dens?
key.title	title for the key
key.xlab	text for the x axis of the key
key.ylab	text for the y axis of the key
key.xtickfun	add text to the ticks of the key x axis
key.ytickfun	add text to the ticks of the key y axis
key.par	parameters for the key
main	the main title of the plot
xlab	main x label
ylab	main y label
lmat	the lmat
lhei	the lhei
lwid	the lwid
extrafun	I do enjoy me some extra fun
linewidth	the width of lines
...	because this function did not already have enough options

Value

a heatmap!

See Also

heatmap.2

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.