Graph of AFMdata object

Source: R/AFMdata.R

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

# S3 method for 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, 5 = legend only

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

See also

AFM.lineProfile

Author

Thomas Gredig

Examples

d = AFM.import(AFM.getSampleImages(type='ibw'))
plot(d, graphType=2, quiet=TRUE)

plot(d, fillOption = "magma", setRange=c(-30,30), quiet=TRUE)


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


# increase the size of the labels:
plot(d, quiet=TRUE) + ggplot2::theme_bw(base_size=16)


# change the name of the z-scale
plot(d, quiet=TRUE) + ggplot2::labs(fill = "h(nm)")