Query banc tables in the CAVE annotation system

Query banc tables in the CAVE annotation system

Usage

banc_cave_query(table, live = TRUE, ...)

Arguments

table

The name of the table (or view, see views section) to query

live

Whether to use live query mode, which updates any root ids to their current value (or to another timestamp when provided). Values of TRUE or 1 select CAVE's Live mode, while 2 selects Live live mode which gives access even to annotations that are not part of a materialisation version. See section Live and Live Live queries for details.

...

Additional arguments passed to flywire_cave_query flywire_cave_query

Value

A data.frame

See also

flywire_cave_query

Examples

# \donttest{
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:nat’:
#> 
#>     intersect, setdiff, union
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
cell_info=banc_cave_query('cell_info')
#> Warning: using default setting
#> Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
#>   requests.exceptions.SSLError: HTTPSConnectionPool(host='global.daf-apis.com', port=443): Max retries exceeded with url: /info/api/v2/datastack/full/brain_and_nerve_cord (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))
#> Run `reticulate::py_last_error()` for details.
#> • Please run dr_fafbseg() to help diagnose.
#> Error in (function (datastack_name = getOption("fafbseg.cave.datastack_name",     "flywire_fafb_production")) {    cavec = check_cave()    client = try(cavec$CAVEclient(datastack_name))    if (inherits(client, "try-error")) {        ui_todo("\nPlease run dr_fafbseg() to help diagnose.")        stop("There seems to be a problem connecting to datastack: ",             datastack_name)    }    client})(datastack_name = datastack_name): There seems to be a problem connecting to datastack: brain_and_nerve_cord
cell_info %>%
  filter(tag2=='anterior-posterior projection pattern') %>%
  count(tag)
#> Error: object 'cell_info' not found
# }