In thomasgredig/nanoscopeAFM: Load and Analyze Atomic Force Microscopy Data Files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 6
)

library(nanoscopeAFM)

Line Profiles

It can be useful to look at a line profile, for example in the height data. You can use AFM.lineProfile() to get an arbitrary line, or AFM.getLine(), if you want to select a horizontal line. In the example below, we provide the coordinates in units of [nm], however, you can also provide the coordinates in pixels, if you set unitPixels to TRUE. Alternatively, if you are not providing any coordinates, you can click on two points to select a profile line.

library(ggplot2)
library(scales)
filename = AFM.getSampleImages(type='tiff')
afmd = AFM.import(filename)
# afmd2 = AFM.lineProfile(afmd)  # click on two points on the image
afmd2 = AFM.lineProfile(afmd, 200,2050, 800,2050, verbose = TRUE)
afmd2 = AFM.lineProfile(afmd2, 200,2080, 800,2080)

plot(afmd2, addLines = TRUE, trimPeaks = 0.01)

This shows where the profile line is measured; the units are in nm, according to the AFM image.

AFM.linePlot(afmd2)
dLine = AFM.linePlot(afmd2, dataOnly = TRUE)
head(dLine)

The line plot has a lowest point at r signif(min(dLine$z),3) nm, and a maximum at r signif(max(dLine$z),3) nm.

thomasgredig/nanoscopeAFM documentation built on Jan. 4, 2023, 1:33 p.m.