plot.AFMdata: Graph of AFMdata object

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

Graph of AFMdata object

Description

By default, trims 1 percent of the outliers in height data

Usage

## S3 method for class 'AFMdata'
plot(
  x,
  no = 1,
  mpt = NA,
  graphType = 1,
  trimPeaks = 0.01,
  fillOption = "viridis",
  addLines = FALSE,
  redBlue = FALSE,
  verbose = FALSE,
  quiet = FALSE,
  setRange = c(0, 0),
  ...
)

Arguments

x	AFMdata object
no	channel number of the image
mpt	midpoint for coloring
graphType	1 = graph with legend outside, 2 = square graph with line bar, 3 = plain graph, 4 = plain graph with scale
trimPeaks	value from 0 to 1, where 0=trim 0% and 1=trim 100% of data points, generally a value less than 0.01 is useful to elevate the contrast of the image
fillOption	can be one of 8 color palettes, use "A" ... "H", see scale_fill_viridis
addLines	if TRUE lines from obj are added to graph, lines can be added with AFM.lineProfile for example
redBlue	if TRUE output red / blue color scheme
verbose	if TRUE it outputs additional information.
quiet	if TRUE then no output at all
setRange	vector with two values, such as c(-30,30) to make the scale from -30 to +30
...	other arguments, such as col='white' to change color of bar

Value

ggplot graph

Author(s)

Thomas Gredig

See Also

AFM.lineProfile

Examples

d = AFM.import(AFM.getSampleImages(type='ibw'))
plot(d, graphType=2)
plot(d, fillOption = "magma", setRange=c(-30,30))

# size will changes the length scale size
plot(d, graphType=4, col='white', size=10)

# increase the size of the labels:
plot(d) + theme_bw(base_size=16)

# change the name of the z-scale
plot(d) + labs(fill = "h(nm)")

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