Remove position-specific lighting bias from side-specific metrics

Under directional light every raised colony is brighter on the side that faces the lamp, whatever the treatment. On a fixed copy stand this bias depends on the colony's position in the frame (TL, TR, BR, BL), so it is estimated from control plates, per position, and subtracted from all plates.

correct_facing_bias(
  colonies,
  control = "control",
  group = "treatment",
  vars = c("delta_MI_facing", "growth_inhibition_pct")
)

Arguments

colonies

Colony table from analyze_plates().

control

Value of group that marks control plates.

group

Column holding the treatment.

vars

Side-specific columns to correct.

Value

colonies with extra columns <var>_corrected.

Examples

d <- data.frame(colony_id = rep(c("TL", "TR"), 4),
                treatment = rep(c("control", "bacteria"), each = 4),
                delta_MI_facing = c(4, -8, 5, -7, 9, -2, 10, -3))
correct_facing_bias(d)
#>   colony_id treatment delta_MI_facing delta_MI_facing_corrected
#> 1        TL   control               4                      -0.5
#> 2        TR   control              -8                      -0.5
#> 3        TL   control               5                       0.5
#> 4        TR   control              -7                       0.5
#> 5        TL  bacteria               9                       4.5
#> 6        TR  bacteria              -2                       5.5
#> 7        TL  bacteria              10                       5.5
#> 8        TR  bacteria              -3                       4.5