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)
heatmap(aba)

# }