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Visualise neurons across multiple Drosophila connectomic datasets in BANC spelunker

Source: R/urls.R
bancsee.Rd

This function constructs a Neuroglancer scene that visualizes neurons from multiple co-registered Drosophila connectomic datasets, including BANC, FAFB, hemibrain, and MANC. It allows for simultaneous visualization of corresponding neurons across these datasets.

Usage

bancsee(
  banc_ids = NULL,
  fafb_ids = NULL,
  hemibrain_ids = NULL,
  manc_ids = NULL,
  nuclei_ids = NULL,
  open = FALSE,
  banc.cols = c("#54BCD1", "#0000FF", "#8A2BE2"),
  fafb.cols = c("#C41E3A", "#FF3131", "#F88379"),
  hemibrain.cols = c("#00FF00", "#32CD32", "#006400"),
  hemibrain.mirrored.cols = c("#FFFF00", "#FFD700", "#FFA500"),
  manc.cols = c("#FFA07A", "#FF4500", "#FF8C00"),
  nulcei.col = "#FC6882",
  url =
    "https://spelunker.cave-explorer.org/#!middleauth+https://global.daf-apis.com/nglstate/api/v1/6431332029693952"
)

Arguments

banc_ids

A vector of neuron IDs from the BANC dataset. Default is NULL.

fafb_ids

A vector of neuron IDs from the FAFB dataset. Default is NULL.

hemibrain_ids

A vector of neuron IDs from the hemibrain dataset. Default is NULL.

manc_ids

A vector of neuron IDs from the MANC dataset. Default is NULL.

nuclei_ids

A vector of nuclei IDs for the BANC dataset. Default is NULL.

open

Logical; if TRUE, the function will open the Neuroglancer scene in a web browser. Default is FALSE.

banc.cols

Vector of hex codes describing a colour spectrum of colors to be interpolated for BANC neurons. Defaults are cyan-purple.

fafb.cols

Vector of hex codes describing a colour spectrum of colors to be interpolated for BANC neurons. Defaults are red hues.

hemibrain.cols

Vector of hex codes describing a colour spectrum of colors to be interpolated for BANC neurons. Defaults green hues.

hemibrain.mirrored.cols

Vector of hex codes describing a colour spectrum of colors to be interpolated for BANC neurons. Defaults are yellow hues.

manc.cols

Vector of hex codes describing a colour spectrum of colors to be interpolated for MANC neurons. Defaults are orange hues.

nulcei.col

Hex code for the colour in which nuclei will be plotted. Default is pink.

url

a spelunker neuroglancer URL.

Value

If open = FALSE, returns a character string containing the URL for the Neuroglancer scene. If open = TRUE, opens the Spelunker Neuroglancer scene in a web browser and invisibly returns the URL.

Details

The function creates a Neuroglancer scene with multiple layers, each corresponding to a different dataset:

  • BANC: "segmentation proofreading" layer

  • FAFB: "fafb v783 imported" layer

  • Hemibrain: "hemibrain v1.2.1 imported" and "hemibrain v1.2.1 imported, mirrored" layers

  • MANC: "manc v1.2.1 imported" layer

  • BANC nuclei: "nuclei (v1)" layer

Each dataset is assigned a unique color palette to distinguish neurons from different sources:

  • BANC: Blue to purple spectrum

  • FAFB: Red spectrum

  • Hemibrain: Green spectrum (original) and Yellow spectrum (mirrored)

  • MANC: Orange spectrum

  • BANC nuclei: Pink

Note

This function suppresses all warnings during execution. While this ensures smooth operation, it may hide important messages. Use with caution and refer to individual function documentation if unexpected behavior occurs.

See also

banc_scene

Examples

if (FALSE) { # \dontrun{
# Visualize cell type DNa01 across datasets
bancsee(banc_ids = c("720575941493078142","720575941455137261"),
        fafb_ids = c("720575940644438551","720575940627787609"),
        hemibrain_ids = c("1170939344"),
        manc_ids = c("10751","10760"),
        open = TRUE)

# Get URL without opening browser
url <- bancsee(banc_ids = c("720575941493078142"),
               fafb_ids = c("720575940644438551"),
               open = FALSE)
} # }