envisionR is an R package designed to facilitate the analysis of experimental data exported from the JAX Envision™ software. This package provides tools for data wrangling, quality control, visualization, and statistical analysis of high-throughput phenomics data.
You can install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("TheJacksonLaboratory/envisionR", build_vignettes = TRUE)library(envisionR)Create URLs to visualize specific moments of video flagged in an analysis:
safety_vidstart <- as.POSIXct("2024-06-15 09:00:00", tz = "US/Central")
envisionR::make_envision_url(org = 9, study = 237, cage = 1819, vidstart = safety_vidstart)Import and clean your data using envisionR functions:
# Importing libraries
library(tidyverse)
library(janitor)
library(ggplot2)
library(here)
library(envisionR)
# Importing annotation data
metadata <- envisionR::envision_metadata(study_name = "Two Drug Study", tzone = "US/Central", lights_on = "06:00:00", lights_off = "18:00:00", study_url = "https://app.murine.net/org/9/study/237/")
annotation <- envisionR::read_annotation_csv("../data/annotation.csv", metadata = metadata)Visualize your data with built-in plotting functions:
# Spaghetti plot
spaghetti_plot(activity_data = activity, metadata = metadata, yvar = "movement_mean_per_cage_cm_s_hour", occupancy_norm = TRUE) + ggokabeito::scale_color_okabe_ito(order = okabe_order)Perform statistical tests and visualize results:
# ANOVA
activity_4hr_post_dose_aov <- aov(baseline_subtract_postdose_0to4hr ~ group_name, data = activity_1min_summarize)
summary(activity_4hr_post_dose_aov)
# Dunnett's Test
library(DescTools)
DunnettTest(x = activity_1min_summarize %>% dplyr::pull(baseline_subtract_postdose_0to4hr), g = activity_1min_summarize %>% dplyr::pull(group_name), control = "Vehicle (0 mg/kg)")Detailed walkthroughs and examples are available in the package vignettes. To view the vignettes, use:
browseVignettes("envisionR")We welcome contributions to the envisionR package. Please fork the repository and submit pull requests for any enhancements or bug fixes.
This package is licensed by The Jackson Laboratory under the GNU General Public License v3.0.
Copyright (C) 2025, The Jackson Laboratory.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
This package was developed by Michael C. Saul, Computational Scientist at The Jackson Laboratory.