scattersmooth {GCDkit} | R Documentation |
Plotting scatterplot with smoothed densities (smoothed two-dimensional histogram) after Eilers & Goeman (2004).
scattersmooth(xlab = NULL, ylab = NULL, samples = NULL, nbin = 100, lambda = 1, pal = heat.colors(100), pch = 15, col = "blue", cex = 0.3, xlim = NULL, ylim = NULL, ...)
xlab, ylab |
character; specification of the plotting variables (formulae OK). |
samples |
character or numeric vector; specification of the samples to be plotted. |
nbin |
integer, giving the number of bins for x and y, or a vector with two integers. |
lambda |
the smoothing parameter; larger lambda gives smoother curves. |
pal |
specification of a palette yielding colours for filled contours. |
pch |
plotting symbols. |
col |
plotting colours. |
cex |
relative size of plotting symbols. |
xlim |
limits of the x axis. |
ylim |
limits of the y axis. |
... |
Further parameters to the original function. |
The function produces a scatterplot with smoothed densities (smoothed two-dimensional histogram).
The code has been adopted, with only small modifications and new interface to GCDkit, from the original R
functions designed by Eilers & Goeman (2004).The original scatterplot function has been renamed
to '.scattersmoothMain
'.
The complete dataset:
If plotted with lambda=1
:
If plotted with lambda=100
:
The variables to be plotted are selected using the function
'selectColumnLabel
'. In the specification of the variables can
be used also arithmetic expressions, see calcCore
for the correct
syntax.
The samples can be selected based on combination of three searching
mechanisms (by sample name/label, range or a Boolean condition) - see
selectSubset
for details.
Returns (invisibly) all parameters calculated by the original function.
The function is NOT Figaro-compatible.
Paul H. C Eilers, p.eilers@erasmusmc.nl
& Vojtěch Janoušek, vojtech.janousek@geology.cz
Eilers PHC, Goeman JJ (2004) Enhancing scatterplots with smoothed densities. Bioinformatics 20: 623-628
data(atacazo) accessVar("atacazo") scattersmooth("SiO2","A/CNK",xlim=c(55,67),ylim=c(0.7,1.2),pal=heat.colors(100),lambda=1) scattersmooth("SiO2","A/CNK",xlim=c(55,67),ylim=c(0.7,1.2),pal=heat.colors(100),pch=17, col="black",cex=1,lambda=100)