afmToolkit (version 1.0.0)

plot.afmdata: Plot an afmdata object

Description

Plots an afmdata object.

Usage

# S3 method for afmdata
plot(x, y = NULL, vs = "Z", segment = "all", ...)

Arguments

x

An object of afmdata class.

y

Variable added for compatibility with plot.

vs

The variable for the x-axis. May take the values "Time" or "Z". It defaults to "Z", plotting thus a Force-Distance curve. If vs is set to "Time", then it plots a Force-Time curve.

segment

The segment of the curve to be plotted. If segment = "all" then all segments of the curve are plotted. Possible values are: "approach", "pause", "retract" and "all".

...

Additional parameters to be pased to the ggplot functions.

Examples

# Loading the data
path <- path.package("afmToolkit")
data <- afmReadJPK("force-save-JPK-3h.txt.gz", path = path)
# Standard plot (out of the box)
plot(data)
# Computing the contact and detach points
data <- afmContactPoint(data, width = 20, mul1 = 1, mul2 = 10)
data <- afmDetachPoint(data, width = 40, mul1 = 3, mul2 = 20)
# Making the baseline correction
data <- afmBaselineCorrection(data)
# Plot once the baseline correction is done
plot(data)
# Plotting only retract segment
plot(data, segment = "retract")
# Plotting the pause segment: Force vs Time
plot(data, segment = "pause", vs = "Time")