heatpairs: Pairwise colored scatterplot based on a two-dimensional...

In stineb/rbeni: Useful R functions for Beni.

Pairwise colored scatterplot based on a two-dimensional Kernel Density Estimation

Description

Pairwise visualization of two dimensional data in a three dimensional fashion facilitating a color encoded Kernel Density Estimation.

Usage

heatpairs(
  mat,
  main = "heatpairs",
  xlim = NULL,
  ylim = NULL,
  labels = NULL,
  add.points = FALSE,
  group = NULL,
  color.group = "magenta",
  method = "spearman",
  colpal = "heat",
  simulate = FALSE,
  daltonize = FALSE,
  cvd = "p",
  alpha = NULL,
  rev = FALSE,
  pch = 19,
  cexplot = 0.5,
  cor.cex = 2.5,
  nrcol = 30,
  grid = 100,
  only = "none",
  add.contour = FALSE,
  nlevels = 10,
  color.contour = "black",
  greyscale = FALSE,
  log = "",
  ...
)

Arguments

mat	a matrix with numerical entries.
main	title(s) of the plot, standard graphics parameter.
xlim	x limits, standard graphics parameter.
ylim	y limits, standard graphics parameter.
labels	a character vector giving the labels to be shown on the diagonal.
add.points	logical: if TRUE (FALSE by default), a certain 'group' of points can be colored in all pairwise plots.
group	indices or rownames of 'mat' to be highlighted in all pairwise plots (not necessarily all).
color.group	R build-in color in which the 'group' of points should be highlighted.
method	a character specifying the correlation method to use ('pearson' (default), 'kendall' or 'spearman').
colpal	a character vector containing R built-in color names or a name of a LSD colorpalette as a character string (see disco() or disco) (defaults to "heat", if not specified).
simulate	logical: if TRUE (FALSE by default), a converted colorpalette is used to simulate dichromat vision according to http://www.daltonize.org (see daltonize).
daltonize	logical: if TRUE (FALSE by default), a converted colorpalette is used to enhance dichromat vision according to http://www.daltonize.org (see daltonize).
cvd	character string implying the type of color vision deficiency ("p" for protanope, "d" for deuteranope or "t" for tritanope).
alpha	alpha value: a two-digit integer between 01 and 99 for color opacity, i.e. appearance of partial or full transparency (usage omitted by default).
rev	logical: if TRUE (FALSE by default), a reversed colorpalette is used.
pch	plotting 'character'. This can either be a single character or an integer code for one of a set of graphics symbols. (see '?pch', to be passed to plot).
cexplot	a numerical value giving the amount by which the points should be magnified relative to the default.
cor.cex	a numerical value giving the amount by which the correlation characters should be magnified relative to the default.
nrcol	a non-negative integer specifying the number of colors to be used (defaults to 100, if not specified).
grid	an integer specifying the size of the grid used for the KDE.
only	a character string which contains 'x' if the density should only be computed for the x axis, 'y' for the y axis (defaults to 'none' for the two-dimensional case).
add.contour	logical: if TRUE (FALSE by default), the contour lines are added to the plot.
nlevels	an integer giving the number of levels of the contour lines.
color.contour	R build-in color for the contour lines.
greyscale	logical: if TRUE (FALSE by default), the used colorpalette is converted to greyscales.
log	a character string which contains "x" if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic.
...	additional parameters to be passed to points and plot

Author(s)

Bjoern Schwalb

See Also

comparisonplot, demotour, disco, colorpalette

Examples

points = 10^4
x = rnorm(points/2)
x = c(x,x+2.5)
y = x + rnorm(points,sd=0.75)
x = sign(x)*abs(x)^1.3
mat = cbind(x,y,x + rnorm(points,sd=0.5))
colnames(mat) = c("x","y","z")
rownames(mat) = 1:nrow(mat)

heatpairs(mat,labels=c(expression(Xi),expression(Lambda),expression(Delta)))

stineb/rbeni documentation built on Feb. 24, 2023, 5:40 a.m.