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Describe the inoculation layout of a plate

Source: R/plate_layout.R
plate_layout.Rd

FunMel uses the known inoculation geometry as a spatial prior. This is what makes it possible to separate several cultures that share one dish, including colonies that touch each other or contact the central fungal mycelium.

Usage

plate_layout(
  n_colonies = 4L,
  radius_frac = 0.45,
  radius_mm = NULL,
  start_deg = -135,
  rotation_deg = 0,
  centre = c("fungus", "none", "bacteria"),
  ids = NULL,
  positions = NULL,
  search_frac = 0.4
)

Arguments

n_colonies

Number of fungal inoculation points placed evenly on a circle (ignored if positions is given).

radius_frac

Distance of the inoculation points from the dish centre, as a fraction of the outer dish radius.

radius_mm

Alternatively, the distance in mm (overrides radius_frac once the dish scale is known).

start_deg

Angle of the first colony, degrees clockwise from 3 o'clock. The default -135 puts the first colony at top-left.

rotation_deg

Extra clockwise rotation of the whole layout.

centre

What is inoculated at the centre: "bacteria", "none" or "fungus". The fungal path fits separate peripheral-target, central- partner and surrounding-zone components; it never adds the central partner to the four target colonies. Hyphal masks are image-based tissue candidates, not inhibition zones.

ids

Colony identifiers.

positions

Optional data frame with columns id, x_rel, y_rel for arbitrary designs.

search_frac

Radius (fraction of the dish radius) around each expected position within which the colony core is searched. Colonies are matched to expected positions closest-first, one colony per position, so search areas may overlap; inoculation points only need to be approximately where the layout says.

Value

An object of class funmel_layout.

Details

Positions are given relative to the dish centre in units of the dish outer radius, with x increasing to the right and y increasing downwards (image convention). The default reproduces the standard four-quadrant design: four fungal colonies on the diagonals at 45 % of the radius (TL = top-left, TR, BR, BL) and, for confrontations, another fungus in the centre.

Always photograph plates in the same orientation (e.g. a mark on the dish rim at 12 o'clock) so that colony IDs are reproducible; otherwise use rotation_deg.

Examples

plate_layout()                      # 4 Zymoseptoria + central fungus
#> <funmel_layout> 4 fungal colonies; centre: fungus
#>  id  x_rel  y_rel
#>  TL -0.318 -0.318
#>  TR  0.318 -0.318
#>  BR  0.318  0.318
#>  BL -0.318  0.318
plate_layout(centre = "none")       # control plate
#> <funmel_layout> 4 fungal colonies; centre: none
#>  id  x_rel  y_rel
#>  TL -0.318 -0.318
#>  TR  0.318 -0.318
#>  BR  0.318  0.318
#>  BL -0.318  0.318
plate_layout(n_colonies = 3, ids = c("A", "B", "C"))
#> <funmel_layout> 3 fungal colonies; centre: fungus
#>  id  x_rel  y_rel
#>   A -0.318 -0.318
#>   B  0.435 -0.116
#>   C -0.116  0.435