From 28776823c5ce1553095e97a5aa2cf6b3765990c0 Mon Sep 17 00:00:00 2001 From: kjkrishnan Date: Fri, 1 Mar 2024 12:46:18 -0500 Subject: [PATCH] Separate cellphonedb and scenic vignettes --- .Rbuildignore | 1 + docs/404.html | 2 + docs/LICENSE-text.html | 2 + .../articles/cellphonedb_vignette.html | 8 + .../articles/articles/tf_scenic_vignette.html | 8 + docs/articles/cellphonedb_vignette.html | 144 ++++++++++ .../empty-anchor.js | 15 + docs/articles/domino2.html | 235 +++++++--------- .../figure-html/unnamed-chunk-4-1.png | Bin 0 -> 496272 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 496272 -> 183056 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 183056 -> 182147 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 182147 -> 167087 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 167087 -> 88225 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 88225 -> 204953 bytes docs/articles/domino_object_vignette.html | 4 +- docs/articles/index.html | 8 +- docs/articles/plotting_vignette.html | 2 + .../figure-html/signalingnet-clusts-1.png | Bin 37911 -> 38762 bytes docs/articles/tf_scenic_vignette.html | 264 ++++++++++++++++++ .../empty-anchor.js | 15 + docs/authors.html | 2 + docs/index.html | 11 +- docs/news/index.html | 2 + docs/old.README.html | 2 + docs/pkgdown.yml | 4 +- docs/reference/add_rl_column.html | 2 + docs/reference/build_domino.html | 2 + docs/reference/circos_ligand_receptor.html | 2 + docs/reference/convert_genes.html | 2 + docs/reference/cor_heatmap-2.png | Bin 24603 -> 24495 bytes docs/reference/cor_heatmap.html | 2 + docs/reference/cor_scatter.html | 2 + docs/reference/count_linkage.html | 2 + docs/reference/create_domino.html | 2 + .../reference/create_regulon_list_scenic.html | 2 + docs/reference/create_rl_map_cellphonedb.html | 2 + docs/reference/do_norm.html | 2 + docs/reference/dom_clusters.html | 2 + docs/reference/dom_correlations.html | 2 + docs/reference/dom_counts.html | 2 + docs/reference/dom_database.html | 2 + docs/reference/dom_de.html | 2 + docs/reference/dom_info.html | 2 + docs/reference/dom_linkages.html | 2 + docs/reference/dom_network_items.html | 2 + docs/reference/dom_signaling.html | 2 + docs/reference/dom_tf_activation.html | 2 + docs/reference/dom_zscores.html | 2 + docs/reference/domino-class.html | 2 + docs/reference/feat_heatmap.html | 2 + docs/reference/gene_network.html | 2 + docs/reference/ggplot_col_gen.html | 2 + .../reference/incoming_signaling_heatmap.html | 2 + docs/reference/index.html | 2 + docs/reference/lc.html | 2 + docs/reference/linkage_summary-class.html | 2 + docs/reference/mean_ligand_expression.html | 2 + .../reference/plot_differential_linkages.html | 2 + docs/reference/print-domino-method.html | 2 + docs/reference/rename_clusters.html | 2 + docs/reference/show-domino-method.html | 2 + docs/reference/signaling_heatmap.html | 2 + docs/reference/signaling_network.html | 2 + docs/reference/summarize_linkages.html | 2 + docs/reference/table_convert_genes.html | 2 + .../reference/test_differential_linkages.html | 2 + docs/search.json | 2 +- docs/sitemap.xml | 6 + index.Rmd | 8 +- index.md | 8 +- inst/pkgdown.yml | 4 +- vignettes/.gitignore | 2 + vignettes/articles/cellphonedb_vignette.Rmd | 37 +++ vignettes/articles/tf_scenic_vignette.Rmd | 144 ++++++++++ vignettes/domino2.Rmd | 129 +-------- 75 files changed, 871 insertions(+), 278 deletions(-) create mode 100644 docs/articles/articles/cellphonedb_vignette.html create mode 100644 docs/articles/articles/tf_scenic_vignette.html create mode 100644 docs/articles/cellphonedb_vignette.html create mode 100644 docs/articles/cellphonedb_vignette_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/domino2_files/figure-html/unnamed-chunk-4-1.png create mode 100644 docs/articles/tf_scenic_vignette.html create mode 100644 docs/articles/tf_scenic_vignette_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 vignettes/.gitignore create mode 100644 vignettes/articles/cellphonedb_vignette.Rmd create mode 100644 vignettes/articles/tf_scenic_vignette.Rmd diff --git a/.Rbuildignore b/.Rbuildignore index 780577f..6fd0f9e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -18,3 +18,4 @@ ^old\.README\.md$ ^readme_images$ ^scenic_bash$ +^vignettes/articles$ diff --git a/docs/404.html b/docs/404.html index c359b27..9f3908c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -47,6 +47,8 @@