plot.barcode: Plot the Persistence Barcode

In archiDART: Plant Root System Architecture Analysis Using DART and RSML Files

Description

Plot the persistence barcode of the topology of a root system. More information can be found in Li et al (2017) and Delory et al (2018).

Usage

## S3 method for class 'barcode'
plot(x, y = NULL, type = "p",  xlim = NULL, ylim = NULL,
        log = "", main = NULL, sub = NULL, xlab = NULL, ylab = NULL,
        ann = par("ann"), axes = TRUE, frame.plot = axes,
        panel.first = NULL, panel.last = NULL, asp = NA,
        xgap.axis = NA, ygap.axis = NA, ...)

Arguments

x	A barcode object. Mandatory.
y	See plot.default
type	See plot.default
xlim	See plot.default
ylim	See plot.default
log	See plot.default
main	See plot.default
sub	See plot.default
xlab	A character string giving a label for the X axis.
ylab	A character string giving a label for the Y axis.
ann	See plot.default
axes	See plot.default
frame.plot	See plot.default
panel.first	See plot.default
panel.last	See plot.default
asp	See plot.default
xgap.axis	See plot.default
ygap.axis	See plot.default
...	Additional graphical parameters.

Value

Returns a plot.

Author(s)

Benjamin M. Delory, Guillaume Lobet

References

Delory B.M., Li M., Topp C.N., Lobet G. (2018). archiDART v3.0: a new data analysis pipeline allowing the topological analysis of plant root systems, F1000Research, 7:22, DOI: doi: 10.12688/f1000research.13541.1

Li M., Duncan K., Topp C.N., Chitwood D.H. (2017) Persistent homology and the branching topologies of plants, American Journal of Botany, DOI: 10.3732/ajb.1700046.

See Also

perhomology, par.

Examples

## Locate folder with RSML file
path <- system.file("extdata", package="archiDART")

table<-rsmlToTable(inputrsml=path, unitlength="cm", rsml.date="age")

#Persistent homology
ph<-perhomology(table)

#Plot the barcode
plot(ph$'monocot-archisimple_1', las=1, xlab="Geodesic distance (cm)")

archiDART documentation built on Feb. 11, 2021, 5:08 p.m.