read.morphml: Return parsed XML or R list versions of a NeuroML file

In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Return parsed XML or R list versions of a NeuroML file

Description

read.morphml is designed to expose the full details of the morphology information in a NeuroML file either as a parsed XML structure processed by the XML package or as an extensively processed R list object. To obtain a neuron object use read.neuron.neuroml.

Usage

read.morphml(f, ..., ReturnXML = FALSE)

Arguments

f	Path to a file on disk or a remote URL (see xmlParse for details).
...	Additional arguments passed to xmlParse
ReturnXML	Whether to return a parsed XML tree (when ReturnXML=TRUE) or a more extensively processed R list object when ReturnXML=FALSE, the default.

Details

NeuroML files consist of an XML tree containing one more or more cells. Each cell contains a tree of segments defining the basic connectivity/position and an optional tree cables defining attributes on groups of segments (e.g. a name, whether they are axon/dendrite/soma etc).

read.morphml will either provide the parsed XML tree which you can query using XPath statements or a more heavily processed version which provides as much information as possible from the segments and cables trees in two R data.frames. The latter option will inevitably drop some information, but will probably be more convenient for most purposes.

Value

Either an R list of S3 class containing one morphml_cell object for every cell in the NeuroML document or an object of class XMLDocument when ReturnXML=TRUE.

References

https://neuroml.org/

See Also

link[XML]{xmlParse}, read.neuron.neuroml

nat documentation built on May 29, 2024, 10:36 a.m.