flywire_connectome_data: Access precomputed flywire connectivity data

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Access precomputed flywire connectivity data

Description

flywire_connectome_data returns a dplyr compatible connection to connectivity dumps on disk.

flywire_connectome_data_version sets the integer version number of the preferred flywire connectome data dump or returns the currently version.

Usage

flywire_connectome_data(
  type = c("syn", "pre", "post"),
  version = NULL,
  cached = TRUE,
  ...
)

flywire_connectome_data_version(set = NULL, default = NA)

Arguments

type	Character vector specifying the kind of data
version	Optional CAVE version. The default value of NULL uses the latest data dump available unless options(fafbseg.flywire_connectome_data_version) has been set (which you can conveniently do using flywire_connectome_data_version()).
cached	When version is NULL whether to use a cached value (lasting 1 hour) of the latest available version.
...	Additional arguments passed to arrow::open_dataset.
set	When set=<number> is passed as an argument the specified data version will be used going forwards in this session as the default. This is achieved by setting the fafbseg.flywire_connectome_data_version option. When set=NA is specified then the option is cleared. When set=FALSE, the latest version on disk will be returned regardless of the value of options("fafbseg.flywire_connectome_data_version")). See examples.
default	A version to return when no other information is available. Defaults to NA to indicate no version information available.

Details

This depends on precomputed data dumps prepared periodically by Sven Dorkenwald. You can download the public release version using the function download_flywire_release_data.

You can download other versions from Sven's Google drive folder. See this FlyWire Slack message for more details and the URL.

Two pieces of information are used to determine the version when it is queried. First the value of options(fafbseg.flywire_connectome_data_version), second the latest available version of the connectivity dumps provided by flywire_connectome_data().

Value

An arrow object that you can use with dplyr verbs like filter in order to find neurons/connectivity data of interest.

An integer version number or a list with the previous value of options(fafbseg.flywire_connectome_data_version) when set=<number>.

See Also

download_flywire_release_data

Examples

# latest available version/
syn=try(flywire_connectome_data('syn'), silent=TRUE)
syn450=try(flywire_connectome_data('syn', version=450), silent=TRUE)
if(!inherits(syn450, 'try-error')) {
syn450
syn450$metadata

dl4ds <- syn450 %>%
  filter(pre_pt_root_id==flywire_ids("DL4_adPN_L", version=450, integer64 = TRUE)) %>%
  collect()
}


## Not run: 
# report active connectome dump version (defaults to most recent available)
flywire_connectome_data_version()

# use the June 2023 public release version as the default
flywire_connectome_data_version(set=630)
# confirm this is the default
flywire_connectome_data_version()

# check the latest version on disk
flywire_connectome_data_version(set=FALSE)

# stop defaulting to specific version (therefore using the latest on disk)
flywire_connectome_data_version(set=NA)
flywire_connectome_data_version()

## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.