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Flexible function for fetching partner data across datasets

Source: R/partners.R
cf_partners.Rd

Flexible function for fetching partner data across datasets

Usage

cf_partners(
  ids,
  threshold = 1L,
  partners = c("inputs", "outputs"),
  bind.rows = TRUE,
  MoreArgs = list(),
  keep.all = FALSE,
  details = c("partner", "query", "both", "neither"),
  use_superclass = getOption("coconatfly.use_superclass", FALSE),
  harmonise_class = getOption("coconatfly.harmonise_class", FALSE)
)

Arguments

ids

A list of ids named by the relevant datasets (see examples) or any other input that can be processed by the keys function (including a hclust dendrogram object.)

threshold

return only edges with at least this many matches. 0 is an option since neuprint sometimes returns 0 weight edges.

partners

Whether to return inputs or outputs

bind.rows

Whether to bind data.frames for each dataset together, keeping only the common columns (default TRUE for convenience but note that some columns will be dropped by unless keep.all=TRUE).

MoreArgs

Additional arguments in the form of a hierarchical list (expert use; see details and examples).

keep.all

Whether to keep all columns when processing multiple datasets rather than just those in common (default=FALSE only keeps shared columns).

details

Which neurons to enrich with metadata. Options:

  • "partner" (default): Add metadata for partner neurons only

  • "query": Add metadata for query neurons only

  • "both": Add metadata for both with .pre/.post suffixes

  • "neither": No metadata, return minimal columns for speed

Metadata can also be added later via cf_add_meta.

use_superclass

If TRUE, rename class/subclass/subsubclass columns to superclass/class/subclass. Can also be set via the coconatfly.use_superclass option.

harmonise_class

If TRUE, harmonise class values to malecns style across all datasets. Can also be set via the coconatfly.harmonise_class option.

Value

A data.frame or a named list (when bind.rows=FALSE)

Details

fancr and fafbseg functions have usually used a > relationship for the threshold, but here (as of May 2024) it is uniformly a >= relationship.

MoreArgs is structured as a list with a top layer naming datasets (using the same long names as cf_datasets. The second (lower) layer names the arguments that will be passed to dataset-specific functions such as fafbseg::flywire_partner_summary2 and malevnc::manc_connection_table.

Examples