Find/predict the soma side or position of male cns neurons.

mcns_somapos returns the XYZ location (in nm, microns or raw voxel space) of the soma position for neurons. When no valid soma position is available, then a NA value is returned.

Usage

mcns_soma_side(ids, method = c("auto", "position", "instance", "manual"))

mcns_somapos(
  ids,
  units = c("nm", "microns", "um", "raw"),
  as_character = FALSE
)

Arguments

ids

A set of bodyids or a dataframe containing the name and somaLocation fields

method

Whether to use the side recorded in the instance field, the soma position or each of those in turn to predict. The method manual returns manually curated soma sides recorded via Clio (see details).

units

For mcns_somapos the units of returned 3D positions. Defaults to nm.

as_character

Whether to return the positions as Nx3 matrix (the default) or as comma separated strings.

Value

For mcns_soma_side a vector of sides (L, R, M, U or NA). Midline or unpaired neurons should be indicated with an M although I have seen U in the past.

For mcns_somapos a matrix or a character vector depending on the value of as_character

Details

the recorded somaSide column in neuPrint / soma_side in clio should be preferred but is not always available. method='auto' will prefer those columns but then cascade through instance and somaLocation to define the rest.

See also

Other annotations: mcns_body_annotations(), mcns_dvid_annotations(), mcns_neuprint_meta()

Examples

# \donttest{
mcns_soma_side('/LAL04.*')
#>  [1] "R" "L" "R" "L" "L" "L" "R" "R" "L" "R" "R" "L" "R" "L" "L" "R" "R" "L" "R"
#> [20] "L" "R" "L" "L" "L" "R" "L" "R" "L" "R" "R" "R" "L" "L" "R"
# }
if (FALSE) { # \dontrun{
# All neurons with a type
table(mcns_soma_side('/.*'), useNA='if')

# compare manual with predictions
mcnswsoma=mcns_body_annotations(query=list(soma_side="exists/1"))
mcnswsoma$pside=mcns_soma_side(mcnswsoma$bodyid)
with(mcnswsoma, table(soma_side, pside))

# compare manual with instance
mcnswsoma=mcns_body_annotations(query=list(soma_side="exists/1"))
mcnswsoma$iside=mcns_soma_side(mcnswsoma$bodyid, method='instance')
with(mcnswsoma, table(soma_side, iside, useNA = 'i'))

# converse: compare instance with manual
mcns_instance=mcns_neuprint_meta('/name:.+')
if(!"somaSide" %in% colnames(mcns_instance))
  mcns_instance$somaSide=mcns_soma_side(mcns_instance, method='manual')
mcns_instance$iside=mcns_soma_side(mcns_instance, method='instance')
# many mismatches e.g. due to neurons without a soma including truncated
# sensory neurons, ascending neurons etc
with(mcns_instance, table(somaSide, iside, useNA = 'i'))

# we can parse that a bit by doing
mcns_instance %>% filter(soma) %>% with(table(somaSide, iside, useNA = 'i'))
} # }
sp=mcns_somapos('/LAL04.*', units='um')
plot(sp[,1:2])

mcns_somapos('LAL042', units='um', as_character=TRUE)
#> [1] "299.768,99.944,128.68" "438.56,87.904,117.6"