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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(nanoscopeAFM)
library(ggplot2)
library(scales)

Loading AFM image

fname = AFM.getSampleImages()[1]
afmd = AFM.import(fname)

The AFM image can be displayed using graphTypes:

graphType 1

This is the basic and default graph for an AFM image:

q = plot(afmd, graphType=1, trimPeaks=0.01)

graphType 2

This graph has a square shape and adds a bar of length 20%; it places the scale inside the graph.

plot(afmd, graphType=2,trimPeaks=0.01)

The image can be saved with ggsave as it is graphed with ggplot.

g1 = plot(afmd, graphType=2, size=10, trimPeaks=0.01)
ggsave(tempfile(pattern = "", fileext = ".png"), plot=g1, dpi=150)

graphType 3

This graph type is bare and has neither length scales nor legend.

plot(afmd, graphType=3, trimPeaks=0.01)
summary(afmd)

graphType 4

This graph type is plain with a scale. You can also change the color and the size of the font that displays the scale.

plot(afmd, graphType=4, col='white', size=10, trimPeaks=0.05, fillOption = 'A')

Red Blue Color Scheme

This graph type is bare and has neither length scales nor legend.

plot(afmd, graphType=1, trimPeaks=0.01, redBlue = TRUE)

Graphing 2 plots side by side

Use the package cowplot to create a graph with two plots. Use save_plot to save the graph.

library(cowplot)
library(latex2exp)
fname2 = AFM.getSampleImages(type='ibw')[1]
afmd = AFM.import(fname2)

g1 = plot(afmd, trimPeaks=0.01, graphType = 1) + 
  labs(fill='h (nm)') + theme(legend.key.size = unit(1, 'char'))
g2 = plot(afmd, no=2, trimPeaks=0.01, graphType = 1, mpt=29.6) +
  labs(fill="A (nm)") + theme(legend.key.size = unit(1, 'char'))
g3 = plot(afmd, no=3, trimPeaks=0.01, graphType = 1, mpt=65.5) +
  labs(fill=TeX("$\\phi$ (deg)")) + theme(legend.key.size = unit(1, 'char'))
g4 = plot(afmd, no=4, trimPeaks=0.01, graphType = 1) + 
  labs(fill="z (nm)") + theme(legend.key.size = unit(1, 'char'))
gAll = plot_grid(g1, g2, g3, g4,
          labels=c('a','b','c','d')) 
ggdraw(add_sub(gAll, 
               "Showing surface morphology of a phthalocyanine thin film\n with (a) height h, (b) amplitude A, (c) phase ϕ, and \n (d) z-sensor z response. Sample / image from Gredig\n Lab, CSU Long Beach.",
               x=0.1, hjust=0))

Changing the Color Palette

You can use the fillOption option to change the color palette, see also ? scale_fill_viridis. There are 8 options:

plot(afmd, graphType = 1, fillOption = "magma")
plot(afmd, graphType = 1, fillOption = "inferno")
plot(afmd, graphType = 1, fillOption = "plasma")
plot(afmd, graphType = 1, fillOption = "viridis")

plot(afmd, graphType = 1, fillOption = "cividis")
plot(afmd, graphType = 1, fillOption = "rocket")
plot(afmd, graphType = 1, fillOption = "mako")
plot(afmd, graphType = 1, fillOption = "turbo")

Adjusting the scale

plot(afmd)
plot(afmd, setRange=c(-50,50))

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