From dd3e001f7788b3bc9ae8b5d32b628ec7112d0be4 Mon Sep 17 00:00:00 2001 From: JP Flores Date: Mon, 22 Jun 2026 19:00:30 -0400 Subject: [PATCH 1/5] Add Plotgardener App docs: Getting Started, Installation, User Interface - Split plotgardenerApp into three structured sub-pages addressing reviewer feedback - Add navbar dropdown for The Plotgardener App - Remove plotgardenerUI vignette, replaced by new App documentation - Update README to correctly name and link The Plotgardener App --- README.md | 6 +- docs/404.html | 19 +- docs/LICENSE-text.html | 21 +- docs/LICENSE.html | 21 +- docs/articles/guides/aesthetics.html | 113 ++--- docs/articles/guides/annotations.html | 131 +++--- .../guides/bioconductor_integration.html | 113 ++--- .../articles/guides/ideograms_and_shapes.html | 131 +++--- .../guides/incorporating_ggplots.html | 279 ++++++------ docs/articles/guides/our_philosophy.html | 23 +- docs/articles/guides/plotgardenerApp.html | 189 ++++++++ .../plotgardenerApp_getting_started.html | 290 +++++++++++++ ...html => plotgardenerApp_installation.html} | 137 +++--- docs/articles/guides/plotgardenerApp_ui.html | 404 ++++++++++++++++++ .../guides/plotgardener_meta_functions.html | 125 +++--- docs/articles/guides/plotgardener_page.html | 125 +++--- .../guides/plotting_multiomic_data.html | 113 ++--- .../guides/reading_data_for_plotgardener.html | 125 +++--- docs/articles/index.html | 29 +- .../introduction_to_plotgardener.html | 113 ++--- docs/authors.html | 49 ++- docs/index.html | 34 +- docs/news/index.html | 21 +- docs/pkgdown.yml | 9 +- docs/reference/annoDomains.html | 49 ++- docs/reference/annoGenomeLabel.html | 53 ++- docs/reference/annoHeatmapLegend.html | 32 +- docs/reference/annoHighlight.html | 21 +- docs/reference/annoPixels.html | 65 ++- docs/reference/annoSegments.html | 51 ++- docs/reference/annoText.html | 21 +- docs/reference/annoXaxis.html | 32 +- docs/reference/annoYaxis.html | 32 +- docs/reference/annoZoomLines.html | 21 +- docs/reference/assembly.html | 21 +- docs/reference/c.html | 21 +- docs/reference/calcSignalRange.html | 21 +- docs/reference/colorby.html | 21 +- docs/reference/defaultPackages.html | 21 +- docs/reference/dot-checkCool.html | 25 +- docs/reference/dot-checkCoolErrors.html | 25 +- docs/reference/dot-coolAutoResolution.html | 25 +- docs/reference/dot-coolRegion.html | 25 +- docs/reference/dot-pullBinChunks.html | 25 +- .../figures/plotgardenerApp-Figure.png | Bin docs/reference/genomes.html | 21 +- docs/reference/index.html | 21 +- docs/reference/mapColors.html | 21 +- docs/reference/pageCreate.html | 21 +- docs/reference/pageGuideHide.html | 21 +- docs/reference/pageGuideHorizontal.html | 21 +- docs/reference/pageGuideShow.html | 21 +- docs/reference/pageGuideVertical.html | 21 +- docs/reference/pageLayoutCol.html | 21 +- docs/reference/pageLayoutRow.html | 21 +- docs/reference/pagePlotPlace.html | 21 +- docs/reference/pagePlotRemove.html | 21 +- docs/reference/pgParams.html | 21 +- docs/reference/plotCircle.html | 21 +- docs/reference/plotGG.html | 27 +- docs/reference/plotGenes.html | 21 +- docs/reference/plotGenomeLabel.html | 56 ++- docs/reference/plotHicRectangle.html | 36 +- docs/reference/plotHicSquare.html | 51 ++- docs/reference/plotHicTriangle.html | 36 +- docs/reference/plotIdeogram.html | 32 +- docs/reference/plotLegend.html | 32 +- docs/reference/plotManhattan.html | 48 ++- docs/reference/plotMultiSignal.html | 36 +- docs/reference/plotPairs.html | 34 +- docs/reference/plotPairsArches.html | 45 +- docs/reference/plotPolygon.html | 21 +- docs/reference/plotRanges.html | 43 +- docs/reference/plotRaster.html | 21 +- docs/reference/plotRect.html | 21 +- docs/reference/plotSegments.html | 51 ++- docs/reference/plotSignal.html | 32 +- docs/reference/plotText.html | 21 +- docs/reference/plotTranscripts.html | 42 +- docs/reference/plotgardener.html | 21 +- docs/reference/readBigwig.html | 36 +- docs/reference/readCool.html | 34 +- docs/reference/readCoolBpResolutions.html | 21 +- docs/reference/readCoolChroms.html | 21 +- docs/reference/readCoolNorms.html | 21 +- docs/reference/readHic.html | 47 +- docs/sitemap.xml | 4 + pkgdown/_pkgdown.yml | 10 +- vignettes/guides/plotgardenerApp.Rmd | 28 ++ .../plotgardenerApp_getting_started.Rmd | 89 ++++ .../guides/plotgardenerApp_installation.Rmd | 63 +++ vignettes/guides/plotgardenerApp_ui.Rmd | 160 +++++++ vignettes/guides/plotgardenerUI.Rmd | 87 ---- 93 files changed, 3660 insertions(+), 1209 deletions(-) create mode 100644 docs/articles/guides/plotgardenerApp.html create mode 100644 docs/articles/guides/plotgardenerApp_getting_started.html rename docs/articles/guides/{plotgardenerUI.html => plotgardenerApp_installation.html} (61%) create mode 100644 docs/articles/guides/plotgardenerApp_ui.html rename man/figures/plotgardenerUI-Figure.png => docs/reference/figures/plotgardenerApp-Figure.png (100%) create mode 100644 vignettes/guides/plotgardenerApp.Rmd create mode 100644 vignettes/guides/plotgardenerApp_getting_started.Rmd create mode 100644 vignettes/guides/plotgardenerApp_installation.Rmd create mode 100644 vignettes/guides/plotgardenerApp_ui.Rmd delete mode 100644 vignettes/guides/plotgardenerUI.Rmd diff --git a/README.md b/README.md index 049cb073..455fb700 100644 --- a/README.md +++ b/README.md @@ -31,12 +31,12 @@ detailed examples and suggested use cases! ## ✨ Desktop App Now Available! -**No R required.** [plotgardenerUI](https://github.com/rishabhsvemuri/pgUI) -is a cross-platform desktop app that brings `plotgardener`'s full +**No R required.** [The Plotgardener App](https://github.com/rishabhsvemuri/ThePlotgardenerApp) +is a desktop application that brings `plotgardener`'s full functionality to a point-and-click interface — no programming experience needed. Build, preview, and export publication-quality genomic figures, then copy the generated R script into any IDE to keep going. -[Learn more →](vignettes/guides/plotgardenerUI.html) +[Learn more →](https://phanstiellab.github.io/plotgardener/articles/guides/plotgardenerApp_getting_started.html) ## Citation diff --git a/docs/404.html b/docs/404.html index 1ff45710..eec607fc 100644 --- a/docs/404.html +++ b/docs/404.html @@ -57,8 +57,23 @@
  • Introduction to plotgardener
    • +
  • + +