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.
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",
...
)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
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.
if TRUE, the only a subset of the full meta data for each neurons is returned with the resulting neuronlist.
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.
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.
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
a data frame, with one entry per neuron queried
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.
if (FALSE) {
# 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)
}