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Query FANC tables in the CAVE annotation system

Source: R/cave.R
fanc_cave_query.Rd

Query FANC tables in the CAVE annotation system

Usage

fanc_cave_query(
  table,
  datastack_name = NULL,
  version = NULL,
  timestamp = NULL,
  live = is.null(version),
  timetravel = FALSE,
  filter_in_dict = NULL,
  filter_out_dict = NULL,
  filter_regex_dict = NULL,
  select_columns = NULL,
  offset = 0L,
  limit = NULL,
  fetch_all_rows = FALSE,
  ...
)

banc_cave_query(
  table,
  datastack_name = NULL,
  version = NULL,
  timestamp = NULL,
  live = is.null(version),
  timetravel = FALSE,
  filter_in_dict = NULL,
  filter_out_dict = NULL,
  filter_regex_dict = NULL,
  select_columns = NULL,
  offset = 0L,
  limit = NULL,
  fetch_all_rows = FALSE,
  ...
)

Arguments

table

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

datastack_name

An optional CAVE datastack_name. If unset a sensible default is chosen.

version

An optional CAVE materialisation version number. See details and examples.

timestamp

An optional timestamp as a string or POSIXct, interpreted as UTC when no timezone is specified.

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.

timetravel

Whether to interpret version/timestamp as a defined point in the past to which the very latest annotations will be sent back in time, recalculating root ids as necessary.

filter_in_dict, filter_out_dict, filter_regex_dict

Optional arguments consisting of key value lists that restrict the returned rows (keeping only matches or filtering out matches). Commonly used to selected rows for specific neurons. See examples and CAVE documentation for details.

select_columns

Either a character vector naming columns or a python dict (required if the query involves multiple tables).

offset

a 0-indexed row number, allows you to page through long results (but see section CAVE Row Limits for some caveats)

limit

whether to limit the number of rows per query (NULL implies no client side limit but there is typically a server side limit of 500,000 rows).

fetch_all_rows

Whether to fetch all rows of a query that exceeds limit (default FALSE). See section CAVE Row Limits for some caveats.

...

Additional arguments passed to flywire_cave_query

Value

A data.frame

See also

flywire_cave_query

Examples

# \donttest{
#nucleus_mar2022=fanc_cave_query(table = "nucleus_mar2022")
neuron_somas_dec2022=fanc_cave_query(table = "neuron_somas_dec2022")
head(neuron_somas_dec2022)
#> # A tibble: 6 × 13
#>      id created             valid target_id id_ref created_ref         valid_ref
#>   <int> <dttm>              <chr>   <int64> <int6> <dttm>              <chr>    
#> 1  7e16 2022-12-19 14:39:30 t          7e16   7e16 2022-12-04 01:45:28 t        
#> 2  7e16 2022-12-19 14:39:30 t          7e16   7e16 2022-12-04 01:45:28 t        
#> 3  7e16 2022-12-19 14:39:30 t          7e16   7e16 2022-12-04 01:45:28 t        
#> 4  7e16 2022-12-19 14:39:30 t          7e16   7e16 2022-12-04 01:45:28 t        
#> 5  7e16 2022-12-19 14:39:30 t          7e16   7e16 2022-12-04 01:45:28 t        
#> 6  7e16 2022-12-19 14:39:30 t          7e16   7e16 2022-12-04 01:45:28 t        
#> # ℹ 6 more variables: volume <dbl>, pt_supervoxel_id <int64>,
#> #   pt_root_id <int64>, pt_position <list<integer>>,
#> #   bb_start_position <list<double>>, bb_end_position <list<double>>
hist(neuron_somas_dec2022$volume)

hist(neuron_somas_dec2022$volume^(1/3))

# }
if (FALSE) { # \dontrun{
points3d(fanc_raw2nm(neuron_somas_dec2022$pt_position), col='red')
} # }
if (FALSE) { # \dontrun{
library(dplyr)
cell_info=banc_cave_query('cell_info')
cell_info %>%
  filter(tag2=='anterior-posterior projection pattern') %>%
  count(tag)
} # }