Read DVID body annotations for fish2 body ids

A thin wrapper around malevnc::manc_dvid_annotations targeting the fish2 dataset. Supports /field:regex query strings to filter annotations locally (see Details).

Usage

fish_dvid_annotations(
  ids = NULL,
  node = "neutu",
  rval = c("data.frame", "list"),
  columns_show = NULL,
  cache = FALSE
)

Arguments

ids

One or more body ids, NULL (default) to fetch all annotations, or a query string (see Details).

node

The DVID node (UUID) to query. The default value of 'neutu' uses the active neutu node i.e. normally the most up to date.

rval

Whether to return a fully parsed "data.frame" (default) or an R "list".

columns_show

Whether to show all columns or only those with a '_user' or '_time' suffix. Accepted values: 'user', 'time', 'all'.

cache

Whether to cache the result for 5 minutes (default FALSE).

Value

A tibble of body annotations. See malevnc::manc_dvid_annotations for column details.

Details

Query string formats for filtering DVID annotations:

"/type:RGC..*"

Match the type field with regex RGC..*.

"RGC.*"

Equivalent shorthand — bare strings default to the type field.

"/status:Traced"

Match a different field.

Regex queries are automatically anchored (^...$) unless the pattern already starts with ^. Queries fetch all annotations (with cache=TRUE) and then filter locally.

For neuprint-based id lookups, use fish_ids instead.

See also

Other live-annotations: fish_annotate()

Examples

# \donttest{
# fetch annotations for specific bodies
fish_dvid_annotations(c(100003384, 100003412))
#> # A tibble: 2 × 11
#>     bodyid connectivity_type per_node_sc status user  group instance type  class
#>      <dbl> <chr>                   <dbl> <chr>  <chr> <int> <chr>    <chr> <chr>
#> 1   1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#> 2   1.00e8 NA                         NA Senso… bergs     0 RGC_R    RGC   NA   
#> # ℹ 2 more variables: keywords <chr>, comment <chr>
# }
if (FALSE) { # \dontrun{
# fetch all annotations using 5m cache if possible
df <- fish_dvid_annotations(cache=TRUE)

# filter by type regex
df <- fish_dvid_annotations("/type:RGC.*", cache=T)
} # }
# \donttest{
# shorthand for type field
df <- fish_dvid_annotations("RGC", cache=T)
df
#> # A tibble: 4,030 × 11
#>     bodyid connectivity_type per_node_sc status user  group instance type  class
#>      <dbl> <chr>                   <dbl> <chr>  <chr> <int> <chr>    <chr> <chr>
#>  1  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#>  2  1.00e8 NA                         NA Senso… bergs     0 RGC_R    RGC   NA   
#>  3  1.00e8 NA                         NA Senso… NA       NA RGC_R    RGC   NA   
#>  4  1.00e8 NA                         NA Senso… bergs     0 RGC_R    RGC   NA   
#>  5  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#>  6  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#>  7  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#>  8  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#>  9  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#> 10  1.00e8 NA                         NA Senso… NA        0 RGC_R    RGC   NA   
#> # ℹ 4,020 more rows
#> # ℹ 2 more variables: keywords <chr>, comment <chr>
# }