Return parsed XML or R list versions of a NeuroML file

Source: R/neuron-io-neuroml.R

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.

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.

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.

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.

See also

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