biosHeatmap: CUSTOMED HEATMAP.2 FOR BIOS USERS
In bedapub/ribiosPlot: Plotting module of ribios for visualization

biosHeatmap

R Documentation

CUSTOMED HEATMAP.2 FOR BIOS USERS

Description

A tailored version of the heatmap.2 function in the gplots package, by giving the default values in the paramter list.

Usage

biosHeatmap(
  x,
  Rowv = TRUE,
  Colv = if (symm) "Rowv" else TRUE,
  distfun = dist,
  hclustfun = function(x) hclust(x, method = "ward.D2"),
  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 = "greenred",
  na.color = "darkgray",
  colsep,
  rowsep,
  sepcolor = "white",
  sepwidth = c(0.05, 0.05),
  cellnote,
  notecex = 1,
  notecol = "cyan",
  trace = c("none", "column", "row", "both"),
  tracecol = "cyan",
  hline = median(breaks),
  vline = median(breaks),
  linecol = tracecol,
  margins = NULL,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  labRow = NULL,
  labCol = NULL,
  cexMain = NULL,
  cexRow = pmin(1, 0.2 + 1/log10(nr)),
  cexCol = pmin(1, 0.2 + 1/log10(nc)),
  ColSideColors,
  RowSideColors,
  color.key.title = "Color Key",
  key = TRUE,
  keysize = 1.5,
  density.info = c("none", "histogram", "density"),
  denscol = tracecol,
  symkey = min(x < 0, na.rm = TRUE) || symbreaks,
  densadj = 0.25,
  zlim,
  lhei = c(1, 7),
  lwid = c(1, 7),
  lmat = NULL,
  ...
)

Arguments

`x`	A matrix
`Rowv`	Logical, whether row-wise dendrogram should be calculated
`Colv`	Logical, whether column-wise dendrogram should be calculated
`distfun`	Function, for calculating distance
`hclustfun`	Function, for hierarchical clustering. By default, the `ward.D2` method is used.
`dendrogram`	Character, specify which dendrogram to be drawn. Note that `Rowv` and `Colv` determines whether dendrograms are calculated and rows or columns are reordered.
`symm`	Logical. Should the matrix be treated as symmetric
`scale`	Logical, should the matrix be row-scaled
`na.rm`	Logical, should NA values should be omitted
`revC`	Logical, should columns be reversed
`add.expr`	Expression
`breaks`	Numeric vector, where to set breaks. Can be missing.
`symbreaks`	Logical, should be breaks symmetric
`col`	Colors for the heatmap, by default green indicates low and red indicates high values
`na.color`	Color for `NA` cells, darkgray by default
`colsep, rowsep`	Integer vector, positions at which columns or rows are separated
`sepcolor, sepwidth`	Color and width of separating lines
`cellnote`	Cell labelling
`notecex`	Cell labelling font size
`notecol`	Cell labelling font color
`trace`	Logical , whether drawing tracing lines, by default not
`tracecol`	Level trace
`hline`	Level trace hline
`vline`	Level trace vline
`linecol`	Level trace color
`margins`	Margins of labs, automatically guessed if no value was provided
`main, xlab, ylab`	Heatmap title, X and Y axis labels
`labRow, labCol`	Row and column labels
`cexMain, cexRow, cexCol`	Title, row and column label font sizes
`ColSideColors, RowSideColors`	Column and row side colors
`color.key.title`	Color key title
`key`	Logical, whether key should be drawn
`keysize`	Key size
`density.info`	Logical, drawing density info in the key histogram, by default not
`denscol`	Logical, should density information be displayed
`symkey`	Logical, should the key be symmetric
`densadj`	densadj
`zlim`	zlim
`lhei`	Heights of rows
`lwid`	Widths of columns
`lmat`	lmat
`...`	Other paramters passed to `heatmap.2` function

Details

Customed version of the heatmap.2, with the common settings used by JItao David Zhang

Value

See heatmap.2 in the gplots package.

Author(s)

Jitao David Zhang <jitao_david.zhang@roche.com>

Examples


set.seed(123)
test <- matrix(rnorm(100), nrow=10)
biosHeatmap(test)

## do not draw row-wise dendrogram
biosHeatmap(test, Rowv=FALSE, dendrogram="column")
## do not draw column-wise dendrogram
biosHeatmap(test, Colv=FALSE, dendrogram="row")
## do not re-sort columns/rows (e.g. for visualization purposes)
biosHeatmap(test, Rowv=FALSE, Colv=FALSE, dendrogram="none")

## define the color range by zlim
biosHeatmap(test, zlim=c(-5, 5))

bedapub/ribiosPlot documentation built on Sept. 1, 2023, 6:50 p.m.