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Predict the group of aedes neurons using type or group information

Source: R/predict-group.R
aedes_predict_group.Rd

Returns a numeric group id for each neuron, preferring its cell type, then its curated group, then its NBLAST cluster and optionally its own serial_id. This is intended for grouping partner neurons in connectivity clustering, e.g. with coconatfly::cf_cosine_plot().

Usage

aedes_predict_group(
  x,
  badtypes = c(NA, "", "undefined", "KCx", "LHN"),
  singletons = FALSE
)

Arguments

x

A data.frame with type, group, nblast_group and serial_id columns, such as returned by aedes_meta() or a partner table from coconatfly::cf_partners() / coconatfly::multi_connection_table() (where these columns describe the partner neurons). Alternatively neuron ids in any form understood by aedes_meta().

badtypes

Values of the type column (after removing any trailing ?) that are too broad or uninformative to define a group.

singletons

Whether neurons without a type, group or NBLAST cluster should fall back to their own serial_id (default FALSE, returning NA). Singleton groups keep connectivity to individual partner neurons (like group = FALSE) but can never match across hemispheres, so they tend to pull left/right homologues apart.

Value

A numeric vector of group ids with one element per row of x (NA for ungroupable neurons unless singletons = TRUE).

Details

All returned ids are serial_id values, so they share one namespace:

  • typed neurons get the smallest serial_id among the rows in x with the same type (so type-derived ids depend on which rows are supplied). A trailing ? is removed before grouping, so e.g. KC4? joins KC4. Types listed in badtypes are ignored.

  • untyped neurons use their group column (itself the smallest serial_id of the group's founding members, see aedes_set_group()). A group of 0 is treated as ungrouped.

  • neurons with no type or group use their nblast_group cluster when this has the form CNNNNN or NNNNN (where NNNNN is the smallest serial_id in the cluster); any leading C is dropped. Surrounding whitespace and a trailing ? are ignored, so " C12345?" is read as 12345. All other nblast_group values are ignored, so a cluster can be struck out by prefixing it with X (e.g. XC12345) without deleting it.

  • neurons with none of these get NA, so that coconatfly drops them as partners, just as it does for group = "group". When singletons = TRUE they instead fall back to their own serial_id, i.e. each becomes a group of one.

Once register_aedes_coconat() has been called, coconatfly metadata for aedes neurons includes the result as a pgroup column, so you can use group = "pgroup" directly in coconatfly functions (see examples).

See also

aedes_set_group(), aedes_meta()

Examples

if (FALSE) { # \dontrun{
library(coconatfly)
x <- multi_connection_table(cf_ids(aedes = "/type:MBON.+"),
  partners = c("in", "out"), threshold = 5, group = FALSE)
x$pgroup <- aedes_predict_group(x)
cf_cosine_plot(x, group = "pgroup")

# coconatfly metadata for aedes neurons already includes a pgroup column
cf_cosine_plot(cf_ids(aedes = "/type:MBON.+"), group = "pgroup")
} # }