smoothScatter: generic for smoothScatter

In tofsims: Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Description

smoothScatter method for PCA class

Usage

smoothScatter(
  x,
  y = NULL,
  nbin = 128,
  bandwidth,
  colramp = colorRampPalette(c("white", blues9)),
  nrpoints = 100,
  ret.selection = FALSE,
  pch = ".",
  cex = 1,
  col = "black",
  transformation = function(x) x^0.25,
  postPlotHook = box,
  xlab = NULL,
  ylab = NULL,
  xlim,
  ylim,
  xaxs = par("xaxs"),
  yaxs = par("yaxs"),
  ...
)

## S4 method for signature 'PCA'
smoothScatter(
  x,
  y = NULL,
  nbin = 128,
  bandwidth,
  colramp = colorRampPalette(c("white", blues9)),
  nrpoints = 100,
  ret.selection = FALSE,
  pch = ".",
  cex = 1,
  col = "black",
  transformation = function(x) x^0.25,
  postPlotHook = box,
  xlab = NULL,
  ylab = NULL,
  xlim,
  ylim,
  xaxs = par("xaxs"),
  yaxs = par("yaxs"),
  ...,
  comps = c(1, 2),
  pcType = "pcaScores",
  label = FALSE,
  labelThreshold = 1
)

Arguments

x	object of class PCA
y	numeric usually NULL
nbin	numeric
bandwidth	numeric vector length 1 or 2
colramp	numeric
nrpoints	numeric
ret.selection	logical
pch	character
cex	numeric
col	character
transformation	function
postPlotHook	box
xlab	NULL
ylab	NULL
xlim	numeric
ylim	numeric
xaxs	par
yaxs	par
...	additional args
comps	numeric
pcType	character
label	boolean
labelThreshold	numeric

Value

graphical output

Examples

library(tofsimsData)
data(tofsimsData)
testImage<-PCAnalysis(testImage, nComp = 4)
smoothScatter(analysis(testImage, 1), comps = c(1,2), 
pcType = 'pcaScores', xlab = 'comp 1', ylab = 'comp 2')

Example output

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth

1

tofsims documentation built on Nov. 8, 2020, 5:10 p.m.