afmToolkit (version 1.0.0)

afmContactPoint: Contact point

Description

Find the contact point in for the Force-Distance curve following the local regression and two thresholds methods described in Microscopy Research and Technique 2013 (see reference).

Usage

afmContactPoint(
  afmdata,
  width = 1,
  mul1,
  mul2,
  lagdiff = width,
  Delta = TRUE,
  loessSmooth = FALSE,
  silent = FALSE
)

Value

An afmdata class variable which will consist on the original input

afmdata variable plus a new list named CP with the following fields:

CP The contact point value.

iCP The position in the array for the contact point value.

delta The delta signal.

noise The noise of the delta signal

Arguments

afmdata

A Force-Distance curve with the afmdata structure. It should be a list with at least the 'data' field with a data frame of at least 4 columns.

width

Width of the window for the local regression (in vector position units)

mul1

First multiplier for the first alarm threshold

mul2

Second multiplier for the second alarm threshold

lagdiff

Lag for estimating the differences in Delta (or slopes) signal. By default it takes the same value as the window with.

Delta

Logical. If TRUE, then the statistic for determining the contact point is the differences between two consecutive values of the slope of the local regression line. If FALSE then the slope itself is used.

loessSmooth

Logical If TRUE, a loess smoothing (via loess.smooth()) is done prior to the determination of the contact point. The span of the smoothing is 0.05 (5 approach segment.

silent

Logical. If TRUE supresses a message showing which curve is being processing (use it when processing a high number of curves). Defaults to FALSE.

References

Benitez R., Moreno-Flores S., Bolos V. J. and Toca-Herrera J.L. (2013). "A new automatic contact point detection algorithm for AFM force curves". Microscopy research and technique, 76 (8), pp. 870-876.

See Also

afmDetachPoint

Examples

path <- path.package("afmToolkit")
data <- afmReadJPK("force-save-JPK-3h.txt.gz", path = path)
width <- 20
mul1 <- 1
mul2 <- 10
data <- afmContactPoint(data, width = width, mul1 = mul1, mul2 = mul2)
if (FALSE) {
plot(data, segment = "approach") + geom_vline(xintercept = data$CP$CP, lty = 2)
}