MycoHalo 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 grow into the halo of the central bacterium.
plate_layout(
n_colonies = 4L,
radius_frac = 0.45,
radius_mm = NULL,
start_deg = -135,
rotation_deg = 0,
centre = c("bacteria", "none", "fungus"),
ids = NULL,
positions = NULL,
search_frac = 0.4
)Number of fungal inoculation points placed evenly on a
circle (ignored if positions is given).
Distance of the inoculation points from the dish centre, as a fraction of the outer dish radius.
Alternatively, the distance in mm (overrides
radius_frac once the dish scale is known).
Angle of the first colony, degrees clockwise from 3 o'clock. The default -135 puts the first colony at top-left.
Extra clockwise rotation of the whole layout.
What is inoculated at the centre: "bacteria", "none"
or "fungus".
Colony identifiers.
Optional data frame with columns id, x_rel, y_rel
for arbitrary designs.
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.
An object of class mycohalo_layout.
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, a bacterium 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.
plate_layout() # 4 Zymoseptoria + central bacterium
#> <mycohalo_layout> 4 fungal colonies; centre: bacteria
#> 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
#> <mycohalo_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"))
#> <mycohalo_layout> 3 fungal colonies; centre: bacteria
#> id x_rel y_rel
#> A -0.318 -0.318
#> B 0.435 -0.116
#> C -0.116 0.435