Get connectivity between ROIs (summary or data frame of connecting neurons)

Get connectivity between ROIs (summary or data frame of connecting neurons)

neuprint_ROI_connectivity(
  rois,
  full = TRUE,
  statistic = c("weight", "count"),
  cached = !full,
  dataset = NULL,
  conn = NULL,
  ...
)

Arguments

rois

regions of interest for a dataset

full

return all neurons involved (TRUE, the default) or give a numeric ROI summary (FALSE)

statistic

either "weight" or count" (default "weight"). Which number to return (see neuprint explorer for details) for summary results (either (when full=FALSE)

cached

pull precomputed results (TRUE) or ask server to recalculate the connectivity (FALSE). Only applicable to summary results when full=FALSE.

dataset

optional, a dataset you want to query. If NULL, the default specified by your R environ file is used or, failing that the current connection, is used. See neuprint_login for details.

conn

optional, a neuprintr connection object, which also specifies the neuPrint server. If NULL, the defaults set in your .Rprofile or .Renviron are used. See neuprint_login for details.

...

methods passed to neuprint_login

Details

When requesting summary connectivity data between ROIs, we recommend setting cached=FALSE. We have noticed small differences in the connections weights, but computation times can get very long for more than a handful of ROIs.

See also

neuprint_simple_connectivity, neuprint_common_connectivity

Examples

# \donttest{
aba <- neuprint_ROI_connectivity(neuprint_ROIs(superLevel = TRUE),full=FALSE)
#> Warning: Dropping missing rois:AB(L) AB(R) AL(L) AL(R) AOTU(R) ATL(L) ATL(R) AVLP(R) BU(L) BU(R) CA(L) CA(R) CAN(R) CRE(L) CRE(R) EB EPA(L) EPA(R) FB FLA(R) GNG GOR(L) GOR(R) IB ICL(L) ICL(R) IPS(R) LAL(L) LAL(R) LH(R) LO(R) LOP(R) ME(R) NO PB PED(R) PLP(R) PRW PVLP(R) SAD SCL(L) SCL(R) SIP(L) SIP(R) SLP(R) SMP(L) SMP(R) SPS(L) SPS(R) VES(L) VES(R) WED(R) a'L(L) a'L(R) aL(L) aL(R) b'L(L) b'L(R) bL(L) bL(R) gL(L) gL(R)
heatmap(aba)

# }