HeatmapOP: Heatmap.

In cbg-ethz/epiNEM: epiNEM

Heatmap.

Description

Heatmap function based on the lattice package more information: ?xyplot

Usage

HeatmapOP(
  x,
  col = "RdYlGn",
  colNA = "grey",
  coln = 11,
  bordercol = "grey",
  borderwidth = 0.1,
  breaks = "sym",
  main = "",
  sub = "",
  dendrogram = "none",
  colorkey = "right",
  Colv = TRUE,
  Rowv = TRUE,
  xrot = 90,
  yrot = 0,
  shrink = c(1, 1),
  cexCol = 1,
  cexRow = 1,
  cexMain = 1,
  cexSub = 1,
  colSideColors = NULL,
  aspect = "fill",
  contour = FALSE,
  useRaster = FALSE,
  xlab = NULL,
  ylab = NULL,
  colSideColorsPos = "top",
  clust = NULL,
  clusterx = NULL,
  axis.padding = 0.5,
  legend = NULL,
  ...
)

Arguments

x	Matrix.
col	Color. See brewer.pal.info for all available color schemes. Alternatively, any number of colors, which are then used to create a color gradient. E.g., c('blue','red') produces a color scheme with a gradient from blue to red.
colNA	color for NAs; defaul is grey
coln	Number of colors.
bordercol	Border color.
borderwidth	Border width.
breaks	Defines the breaks in the color range. "sym" makes the breaks symmetric around 0.
main	Main title.
sub	Subtitle.
dendrogram	Draw dendrogram with "both", "col" or "row", or do not draw with "none".
colorkey	Draw colorkey "left", "right" (default), "top", "bottom" or NULL for no colorkey. See ?lattice::levelplot for more complex colorkey options.
Colv	Cluster columns (TRUE) or not (FALSE).
Rowv	Cluster rows (TRUE) or not (FALSE).
xrot	Rotate the column names by degree.
yrot	Rotate the row names by degree.
shrink	c(x,y) defines a range of size for the data boxes from low to high.
cexCol	Font size of column names.
cexRow	Font size of row names.
cexMain	Font size of main title.
cexSub	Font size of subtitle.
colSideColors	Defines a numeric vector to annotate columns with different colors.
aspect	"iso" for quadratic boxes or "fill" for streched boxes.
contour	TRUE adds a contour plot.
useRaster	TRUE to add raster visuals
xlab	Label for the x-axis.
ylab	Label for the y-axis.
colSideColorsPos	Place colSideColors at the "top" or "bottom".
clust	p, s, or k for correlation clustering
clusterx	Optional data matrix y with the same dimensions as x. x's columns or rows are sorted by the cluster information of y. Col- and rownames of y must be in the same order as in x.
axis.padding	padding around the heatmap (0.5 is no padding, default)
legend	list obejct. For parameters see base function ?legend for details. x and y parameters are relative to the inside of the heatmap and are between 0 and 1. E.g., to place the legend outside of the heatmap x and y need to be either less than 0 or greater than 1.
...	Optional arguments.

Value

lattice object/matrix

Author(s)

Martin Pirkl & Oscar Perpinan at http://oscarperpinan.github.io/rastervis/

Examples

x <- matrix(rnorm(50), 10, 5)
HeatmapOP(x, dendrogram = "both", aspect = "iso", xrot = 45)

cbg-ethz/epiNEM documentation built on Nov. 6, 2024, 4:21 a.m.