Package index • grayleafspotr

Analysis pipeline

Run the SmallUNet segmentation pipeline on plate images.

grayleafspot_run(): Run the gray leaf spot pipeline — simplified entry point
grayleafspot_analyze(): Analyze plate images with the SmallUNet pipeline
grayleafspot_download_model(): Download the SmallUNet segmentation model
grayleafspot_python_available(): Check whether the Python ML dependencies are available
grayleafspot_python_executable(): Return the Python executable used by the grayleafspot pipeline

Load, save, and convert run results.

read_grayleafspot_results(): Read a saved grayleafspot run from disk
write_grayleafspot_results(): Write grayleafspot results to disk
as_grayleafspot_growth_data(): Coerce a grayleafspot run object to a tidy data frame
example_grayleafspot_results(): Load the built-in example grayleafspot run

Template ggplot2 visualisations — all return a ggplot object.

plot_colony_expansion(): Plot colony expansion over time
plot_growth_roughness(): Plot relative growth rate and edge roughness
plot_stress_remodeling(): Plot crack coverage and crack count over time
plot_texture_organization(): Plot texture entropy and center-to-edge intensity delta over time
plot_shape_vs_stress(): Scatter plot of colony shape vs crack stress
plot_radial_growth_area(): Plot radial growth rate and colony area by plate over time
plot_feature_heatmap(): Pearson correlation heatmap of numeric morphology features
plot_radial_profile(): Plot the radial intensity profile from the first image in a run