R: Visualize two-dimensional data clusters (add to an existing...

singleclusterplot {LSD}

R Documentation

Visualize two-dimensional data clusters (add to an existing plot)

Description

Depict a numeric matrix or list utilizing the underlying distribution quantiles of one dimension in a color encoded fashion (add to an existing plot).

Usage

singleclusterplot(
  input,
  at = NULL,
  fromto = c(0.05, 0.95),
  colpal = "standardheat",
  simulate = FALSE,
  daltonize = FALSE,
  cvd = "p",
  nrcol = 25,
  outer.col = "lightgrey",
  rev = FALSE,
  alpha = NULL,
  quartiles.col = c("grey", "black", "grey"),
  add.quartiles = TRUE
)

Arguments

`input`	matrix or list with numerical entries.
`at`	a integer vector containing the x-positions corresponding to the columns of 'input'.
`fromto`	a numeric vector containing the range of quantiles (between 0 and 1) to be plotted.
`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`).
`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).
`nrcol`	a non-negative integer specifying the number of colors to be used (defaults to 25, if not specified).
`outer.col`	R built-in color to be used for outlier lines (lines outside of 'fromto').
`rev`	logical: if `TRUE` (`FALSE` by default), a reversed colorpalette is used.
`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).
`quartiles.col`	a character vector containing three R built-in colors for quartile lines (c('0.25','0.5','0.75')).
`add.quartiles`	logical: if `TRUE` (by default), lines are plotted corresponding to the quartiles.

Author(s)

Achim Tresch, Bjoern Schwalb

Examples

samples = 100
probes = 200
clus = matrix(rnorm(probes*samples,sd=1),ncol=probes)

clus = rbind(
	t(t(clus)+sin(1:probes/10))+1:nrow(clus)/samples,
	t(t(clus)+sin(pi/2+1:probes/10))+1:nrow(clus)/samples)

emptyplot(xlim = c(1,ncol(clus)),ylim = range(clus))
singleclusterplot(clus)
axis(1)
axis(2)
box()