afmToolkit (version 1.0.0)

afmBaselineCorrection: Performs a baseline correction to an AFM F-z curve

Description

This function performs the baseline correction to an AFM F-z curve within an afmdata structure.

It substracts a best fit line to the cuve: for the approach and contact segments, it fits a line to the approach curve points where for which |z|>ZPointApp and for the retract segment, it fits a line to the retract curve where |z|> ZpointRet.

If no ZPointApp is given and the contact point has been already estimated (via afmContactPoint() function), then it is found as $$ ZPointApp = 0.7 ContactPoint + 0.3 max(Z) $$

Usage

afmBaselineCorrection(
  afmdata,
  ZPointApp = NULL,
  ZPointRet = NULL,
  fitpause = c("approach", "retract", "none"),
  vsTime = FALSE,
  sinusoidal = FALSE
)

Value

afmdata An afmdata structure identical to the one in the input, but with an additional ForceCorrected column in the

data dataframe of the afmdata structure.

Arguments

afmdata

An afmdata structure.

ZPointApp

Point in the approach segment of the curve that defines the approach baseline

ZPointRet

Point in the retract segment of the curves that defines the retract baseline

fitpause

Behaviour for the baseline correction at the pause segment: if "approach" (default), the pause segment is correted using the best line fit done on the approach segment, if "retract" the best line fit of the retract segment is used, if "none", no baseline correction is done on the pause segment.

vsTime

Logical. If TRUE then the baseline correction is performed following the Force vs time approach described by S. Moreno-Flores (Moreno Flores (2016)).

sinusoidal

Logical. If TRUE, then a pure harmonic is added to the fit of the baseline in order to remove possible periodical noise. Defaults to FALSE.

References

Moreno Flores (2016). Baseline correction of AFM force curves in the force-time representation. Microscopy Research and Technique, 79, (11), pp. 1045-1049.

Examples

AFMcurve <- afmReadJPK("force-save-JPK-2h.txt.gz", path = path.package("afmToolkit"))
ZPointApp <- 6.43e-6
ZPointRet <- 6.45e-6
AFMcurve <- afmBaselineCorrection(AFMcurve,ZPointApp = ZPointApp,ZPointRet = ZPointRet)
plot(AFMcurve)

# Without providing ZPointApp
AFMcurve <- afmReadJPK("force-save-JPK-3h.txt.gz", path = path.package("afmToolkit"))
AFMcurve <- afmContactPoint(AFMcurve,width = 10,mul1 = 1,mul2 = 20, 
                             loessSmooth = FALSE)
AFMcurve <- afmBaselineCorrection(AFMcurve)
plot(AFMcurve)