neuromorpho_neurons_meta: Get some of the meta data associated with a neuron

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

Get some of the meta data associated with a neuron

Description

Retrieve some the meta data associated with query neurons, in a compact way. Neurons can be queried using either their neuron ID or their name.

Usage

neuromorpho_neurons_meta(
  neuron_name = NULL,
  neuron_id = NULL,
  light = TRUE,
  progress = TRUE,
  batch.size = 10,
  neuromorpho_url = "http://neuromorpho.org",
  ...
)

neuromorpho_neuron_meta(
  neuron_name = NULL,
  neuron_id = NULL,
  light = TRUE,
  neuromorpho_url = "http://neuromorpho.org",
  ...
)

Arguments

neuron_name	a neuron name, or vector of neuron names, as recorded in the neuromorpho database. Names and neuron IDs can be found by searching the repository, for example via neuromorpho_search
neuron_id	a neuron ID, or vector of neuron IDs, as recorded in the neuromorpho database. If neuron_name is given this supersedes neuron_id, which is then treated as if its value were NULL.
light	if TRUE, the only a subset of the full meta data for each neurons is returned with the resulting neuronlist.
progress	if TRUE or a numeric value, a progress bar is shown. The bar progresses when each batch is completed. If TRUE, or 100, the bar completes where all batches are done.
batch.size	the number of requests sent at once to the neuromorpho.org, using multi_run. Requests are sent to neuromorpho.org in parallel to speed up the process of reading neurons. Batches of queries are processed serially. Increasing the value of batch.size may reduce read time.
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

The meta data for reconstructions has been extracted by neuromorpho.org from corresponding publications. Some of these neuron fields will have multiple entries, for example there might be multiple designations for a cell type, or brain region, or multiple labs count be credited for a neuron's reconstruction. This function returns the majority of the information stored on neuromorpho.org for a given set of neurons, but collapses some field entries into one field entry, so we can use a simpler data structure (a data.frame) to represent this information, rather than a list. This is useful for adding to neuronlist objects as an attribute, as is standard in nat family packages. If light = TRUE, then only the following information is returned in the final data frame:

• neuron_id

• neuron_name

• species

• brain_region

• cell_type

• archive

Use neuromorpho_neurons_info if you need the full complement of information for a neuron.

Value

a data frame, with one entry per neuron queried

See Also

neuromorpho_search, neuromorpho_neurons_info, neuromorpho_fields

Examples

## Not run: 
# These are some names for a few elephant neurons
elephant_neuron_names = c("155-2-1Stel", "155-2-2Stel", "155-2-5Stel")

# We can now get the meta information associated with these reconstructions
elephant_neuron_info = neuromorpho_neurons_info(elephant_neuron_names)

# We can get essentially the same information as a data frame instead
elephant_neuron_meta = neuromorpho_neurons_meta(elephant_neuron_names)

## End(Not run)

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