Package: grayleafspotr 0.99.15

Rohan R

grayleafspotr: Quantitative Analysis of Gray Leaf Spot Colonies from Plate Images

Quantitative phenotyping of gray leaf spot (Magnaporthe oryzae) fungal colonies grown on petri dishes. The package segments colonies from time-lapse plate photographs using a bundled SmallUNet deep-learning model, extracts morphometric and texture features (area, eccentricity, crack coverage, radial profile), and provides tidy result objects together with template ggplot2 visualisations. Python dependencies are managed automatically through basilisk; no manual environment setup is required.

Authors:Rohan R [aut, cre, cph]

grayleafspotr_0.99.15.tar.gz
grayleafspotr_0.99.15.zip(r-4.7-any)grayleafspotr_0.99.15.zip(r-4.6-any)grayleafspotr_0.99.15.zip(r-4.5-any)
grayleafspotr_0.99.15.tgz(r-4.6-any)grayleafspotr_0.99.15.tgz(r-4.5-any)
grayleafspotr_0.99.15.tar.gz(r-4.7-any)grayleafspotr_0.99.15.tar.gz(r-4.6-any)
grayleafspotr_0.99.15.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
grayleafspotr/json (API)

# Install 'grayleafspotr' in R:

install.packages('grayleafspotr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rotsl/grayleafspotr/issues

Pkgdown/docs site:https://rotsl.github.io

On BioConductor:grayleafspotr-0.99.14(bioc 3.24)

software preprocessing visualization classification featureextraction bioconductor bioconductor-package biological-data-analysis grayleafspot huggingface image-processing ml python r-universe segmentation

4.85 score 1 stars 6 scripts 167 downloads 18 exports 91 dependencies

Last updated from:37200214f3. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	156
linux-devel	OK	454
source / vignettes	OK	1593
linux-release	OK	351
macos-release	OK	293
macos-oldrel	OK	281
windows-devel	OK	243
windows-release	OK	205
windows-oldrel	OK	227
wasm-release	OK	132

Exports:as_grayleafspot_growth_data example_grayleafspot_results grayleafspot_analyze grayleafspot_download_model grayleafspot_python_available grayleafspot_python_executable grayleafspot_run plot_colony_expansion plot_feature_heatmap plot_grayleafspot_overlay plot_growth_roughness plot_radial_growth_area plot_radial_profile plot_shape_vs_stress plot_stress_remodeling plot_texture_organization read_grayleafspot_results write_grayleafspot_results

Dependencies:abind askpass base64enc basilisk BiocFileCache BiocGenerics bit bit64 bitops blob bslib cachem cli clipr cpp11 crayon curl DBI dbplyr digest dir.expiry dplyr EBImage evaluate farver fastmap fftwtools filelock fontawesome fs generics ggplot2 glue gtable here highr hms htmltools htmlwidgets httr2 isoband jpeg jquerylib jsonlite knitr labeling lattice lifecycle locfit magrittr Matrix memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppTOML RCurl readr reticulate rlang rmarkdown rprojroot RSQLite S7 sass scales stringi stringr sys tibble tidyr tidyselect tiff tinytex tzdb utf8 vctrs viridisLite vroom withr xfun yaml

Getting Started with grayleafspotr

Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-10-10
Started: 2026-04-28

grayleafspotr Workflow

Rendered fromgrayleafspotr-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-10-10
Started: 2026-04-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Coerce a grayleafspot run object to a tidy data frame	as_grayleafspot_growth_data
Load the built-in example grayleafspot run	example_grayleafspot_results
Analyze plate images with the SmallUNet pipeline	grayleafspot_analyze
Download the SmallUNet segmentation model	grayleafspot_download_model
Check whether the Python ML dependencies are available	grayleafspot_python_available
Return the Python executable used by the grayleafspot pipeline	grayleafspot_python_executable
Run the gray leaf spot pipeline — simplified entry point	grayleafspot_run
Plot colony expansion over time	plot_colony_expansion
Pearson correlation heatmap of numeric morphology features	plot_feature_heatmap
Overlay detected regions of interest on a plate image	plot_grayleafspot_overlay
Plot relative growth rate and edge roughness	plot_growth_roughness
Plot radial growth rate and colony area by plate over time	plot_radial_growth_area
Plot the radial intensity profile from the first image in a run	plot_radial_profile
Scatter plot of colony shape vs crack stress	plot_shape_vs_stress
Plot crack coverage and crack count over time	plot_stress_remodeling
Plot texture entropy and center-to-edge intensity delta over time	plot_texture_organization
Read a saved grayleafspot run from disk	read_grayleafspot_results
Write grayleafspot results to disk	write_grayleafspot_results