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Plot plate-level darkness and matched melanization coefficients

Source: R/plot-comparison.R
plot_treatment_comparison.Rd

A two-panel descriptive figure. Panel A shows independent plate MI means and control means within each matching set. Panel B shows treatment plate ratios and the set-specific ratio of means. Bars show descriptive between-plate SD, never confidence intervals. Single-plate SD is unavailable. Ratio SD conditions on the shared control mean and does not quantify its uncertainty. Controls shown on multiple rows within a set are shared, not new replicates.

Usage

plot_treatment_comparison(
  colonies,
  control = "control",
  by = NULL,
  preview = FALSE,
  labels = NULL,
  file = NULL,
  width = 7.2,
  height = NULL,
  palette = NULL,
  require_qc = FALSE,
  caption = c("none", "brief", "full")
)

Arguments

colonies

Colony table, batch result, project object, current project folder, project.rds or saved analysis RDS. Projects use current metadata; directly selected analysis files use their stored metadata snapshot.

control

Control treatment label.

by

Additional matching columns passed to melanization_coefficient().

preview

TRUE labels the figure as a provisional preview. No metadata approval flags are required in either mode. Unconfirmed image QC warns by default and is labelled in the caption.

labels

Optional named character vector of treatment display names.

file

Optional output prefix. Writes vector PDF and SVG and 600-dpi PNG.

width, height

Export dimensions in inches. Height defaults to row count.

palette

Optional named vector of treatment colours. Controls always use dark outlined squares; treatments use filled circles.

require_qc

Default FALSE warns on unconfirmed recorded QC. TRUE requires every included plate to have qc_pass=TRUE.

caption

Text beneath the figure: none (default), brief, or full. The full explanation remains in the FunMel_caption attribute and is exported separately as _caption.txt. QC warnings and statistical safeguards remain.

Value

A ggplot object, invisibly when exported. Colours and typography can be edited using standard ggplot2 methods. Match the target journal's size and caption requirements before submission. The attribute FunMel_statistics contains the plotted means, SDs, counts and descriptive differences. Export also writes a _statistics.csv companion table.

Details

A project or finalized result awaiting matching assignments returns invisible NULL with an informative message; no comparison file is created. Saved results awaiting target-measurement review also return invisible NULL with the affected plate/colony IDs. Complete target measurements are required.