plot.barcode {archiDART}

Plot the Persistence Barcode

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)")