You can install the development version of mapashiny like so:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
remotes::install_github(
"jaspershen-lab/mapashiny",
dependencies = TRUE,
repos = BiocManager::repositories(),
upgrade = "ask"
)
#> Using GitHub PAT from the git credential store.
#> Downloading GitHub repo jaspershen-lab/mapashiny@HEAD
#> rprojroot (2.0.4 -> 2.1.1 ) [CRAN]
#> xfun (0.52 -> 0.53 ) [CRAN]
#> evaluate (1.0.3 -> 1.0.5 ) [CRAN]
#> Rcpp (1.0.14 -> 1.1.0 ) [CRAN]
#> commonmark (1.9.5 -> 2.0.0 ) [CRAN]
#> later (1.4.2 -> 1.4.4 ) [CRAN]
#> utf8 (1.2.5 -> 1.2.6 ) [CRAN]
#> pillar (1.10.2 -> 1.11.0 ) [CRAN]
#> tibble (3.2.1 -> 3.3.0 ) [CRAN]
#> curl (6.2.3 -> 7.0.0 ) [CRAN]
#> GenomeInfoDb (1.44.0 -> 1.44.2 ) [CRAN]
#> KEGGREST (1.48.0 -> 1.48.1 ) [CRAN]
#> RSQLite (2.3.11 -> 2.4.3 ) [CRAN]
#> purrr (1.0.4 -> 1.1.0 ) [CRAN]
#> yulab.utils (0.2.0 -> 0.2.1 ) [CRAN]
#> cowplot (1.1.3 -> 1.2.0 ) [CRAN]
#> data.table (1.17.4 -> 1.17.8 ) [CRAN]
#> ggforce (0.4.2 -> 0.5.0 ) [CRAN]
#> fgsea (1.34.0 -> 1.34.2 ) [CRAN]
#> BiocParallel (1.42.0 -> 1.42.1 ) [CRAN]
#> patchwork (1.3.0 -> 1.3.2 ) [CRAN]
#> ggtree (3.16.0 -> 3.16.3 ) [CRAN]
#> scatterpie (0.2.4 -> 0.2.5 ) [CRAN]
#> ggtangle (0.0.6 -> 0.0.7 ) [CRAN]
#> ggnewscale (0.5.1 -> 0.5.2 ) [CRAN]
#> ggfun (0.1.8 -> 0.2.0 ) [CRAN]
#> aplot (0.2.5 -> 0.2.8 ) [CRAN]
#> waldo (0.6.1 -> 0.6.2 ) [CRAN]
#> xml2 (1.3.8 -> 1.4.0 ) [CRAN]
#> shiny (1.10.0 -> 1.11.1 ) [CRAN]
#> parallelly (1.44.0 -> 1.45.1 ) [CRAN]
#> BiocManager (1.30.25 -> 1.30.26) [CRAN]
#> BiocFileC... (2.16.0 -> 2.16.2 ) [CRAN]
#> spelling (2.3.1 -> 2.3.2 ) [CRAN]
#> future (1.49.0 -> 1.67.0 ) [CRAN]
#> Cairo (1.6-2 -> 1.6-5 ) [CRAN]
#> Annotatio... (3.16.0 -> 3.16.1 ) [CRAN]
#> Installing 37 packages: rprojroot, xfun, evaluate, Rcpp, commonmark, later, utf8, pillar, tibble, curl, GenomeInfoDb, KEGGREST, RSQLite, purrr, yulab.utils, cowplot, data.table, ggforce, fgsea, BiocParallel, patchwork, ggtree, scatterpie, ggtangle, ggnewscale, ggfun, aplot, waldo, xml2, shiny, parallelly, BiocManager, BiocFileCache, spelling, future, Cairo, AnnotationHub
#>
#> The downloaded binary packages are in
#> /var/folders/6d/g00_j1mn3wddb038xh8zrn6h0000gn/T//RtmpBLrSoE/downloaded_packages
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> checking for file ‘/private/var/folders/6d/g00_j1mn3wddb038xh8zrn6h0000gn/T/RtmpBLrSoE/remotes1615423e11a66/jaspershen-lab-mapashiny-254c99a/DESCRIPTION’ ... ✔ checking for file ‘/private/var/folders/6d/g00_j1mn3wddb038xh8zrn6h0000gn/T/RtmpBLrSoE/remotes1615423e11a66/jaspershen-lab-mapashiny-254c99a/DESCRIPTION’
#> ─ preparing ‘mapashiny’:
#> checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
#> ─ excluding invalid files
#> Subdirectory 'R' contains invalid file names:
#> ‘_disable_autoload.R’
#> ─ checking for LF line-endings in source and make files and shell scripts
#> ─ checking for empty or unneeded directories
#> ─ building ‘mapashiny_1.1.0.tar.gz’
#>
#> You can launch the application by running:
mapashiny::run_mapa_shiny()You are reading the doc about version : 1.1.0
This README has been compiled on the
Sys.time()
#> [1] "2025-08-31 12:29:53 +08"Here are the tests results and package coverage:
# devtools::check(quiet = TRUE)covr::package_coverage()
#> mapashiny Coverage: 49.65%
#> R/run_app.R: 0.00%
#> R/5_pathway_similarity.R: 42.61%
#> R/8_llm_interpretation.R: 46.43%
#> R/4_enrich_pathway.R: 49.89%
#> R/9_data_visualization.R: 50.53%
#> R/3_upload_data.R: 52.57%
#> R/10_results.R: 53.85%
#> R/6_pathway_clustering.R: 54.47%
#> R/app_server.R: 97.67%
#> R/app_config.R: 100.00%
#> R/app_ui.R: 100.00%