neuromorpho_search: Make a custom neuron search to the neuromorpho.org repository

In jefferislab/neuromorphr: R client utilities for interacting with the NeuroMorpho online repository for neuron morphology data

Make a custom neuron search to the neuromorpho.org repository

Description

Search for neurons in the neuromorpho.org repository. The returned data frame can be used to get neuron IDs and neuron names, that can be fed to neuromorpho_read_neurons, in order to read neurons from neuromorpho.org. Searches are made by looking at the meta data for neurons in the repositroy, i.e. querying for certain entries in certain neuron fields.

Usage

neuromorpho_search(
  search_terms = c("archive:Jacobs", "species:elephant", "brain_region:cerebellum"),
  neuromorpho_url = "http://neuromorpho.org",
  ...
)

Arguments

search_terms	a vector of search terms, with each term formatted as "field:field entry". All valid neuron fields can be seen by calling neuromorpho_fields, and all the entries for certain fields can be seen using neuromorpho_fields_entries. Only meta data for neurons that have the entries described for all given search terms will be returned. To find neurons that are in either of two field entries, one can use, for example, "species:rat,mouse" to return all rat or mouse neurons.
neuromorpho_url	the base URL for querying the neuromorpho database, defaults to http://neuromorpho.org
...	methods passed to neuromorpho_async_req, or in some cases, neuromorphr:::neuromorpho_fetch

Details

All the data fields, and their entries, can be seen and explored on neuromorpho.org at http://neuromorpho.org/MetaData.jsp.

Value

a data data frame, where each entry is a neuron matching the query specifications.

See Also

neuromorpho_field_entries, neuromorpho_read_neurons, neuromorpho_fields

jefferislab/neuromorphr documentation built on April 25, 2023, 9:07 p.m.