Merge pull request #836 from josschavezf/suite_modular

update dropdown menu
drieslab · Dec 4, 2023 · 1325f3f · 1325f3f
2 parents 6480cdc + d77e61b
commit 1325f3f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,15 +6,17 @@ Authors@R: c(
 		 role = c("aut", "cre")),
 	person("Jiaji", "George Chen", email = "[email protected]",
 		 role = c("aut")),
-	person("Natalie", "Del Rossi", email = "[email protected]",
-		 role = c("aut")),
+	person("Joselyn C.", "Chávez-Fuentes", email = "[email protected]",
+		 role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
 	person("Guo-Cheng", "Yuan", email = "[email protected]",
 		 role = c("aut")),
     person("Matthew", "O'Brien", email = "[email protected]",
 		 role = c("aut")),
-	person("Joselyn C.", "Chávez-Fuentes", email = "[email protected]",
-		 role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
 	person("Edward", "Ruiz", email = "[email protected]",
+		 role = c("aut")),
+	person("Wen", "Wang", email = "[email protected]",
+		 role = c("aut")),
+	person("Natalie", "Del Rossi", email = "[email protected]",
 		 role = c("aut"))
 	)
 Maintainer: Ruben Dries <[email protected]>

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -10,7 +10,7 @@ authors:
 
 
 template:
-  bootstrap: 5
+  bootstrap: 3
   bslib:
     bg: "#FFFFFF"
     fg: "#000000"
@@ -44,8 +44,16 @@ navbar:
         href: articles/object_creation.html
       - text: Giotto Class Structure
         href: articles/structure.html
+      - text: Giotto Class Structure
+        href: articles/structure.html
+      - text: Solutions to Installation Errors
+        href: articles/errorsfaqsandtips.html
+      - text: FAQs
+        href: articles/faqs.html
       - text: Branches
         href: articles/branches.html
+      - text: How to report a bug
+        href: articles/github_issues.html
     reference:
       text: Documentation
       href: reference/index.html
@@ -87,64 +95,76 @@ navbar:
       text: Examples
       menu:
       - text: Seq-Scope
-      - text: Mouse liver
-        href: articles/seqscope_mouse_liver.html
+        menu:
+        - text: Mouse liver
+          href: articles/seqscope_mouse_liver.html
       - text: -------
       - text: Visium
-      - text: Visium Mouse Kidney
-        href: articles/visium_mouse_kidney.html
-      - text: Visium Mouse Brain
-        href: articles/visium_mouse_brain.html
-      - text: Visium Prostate Integration
-        href: articles/visium_prostate_integration.html
-      - text: CytAssist Human Lung Cancer
-        href: articles/visium_cytassist_lungcancer.html
-      - text: CytAssist Multi-omics Human Glioblastoma
-        href: articles/visium_cytassist_human_glioblastoma.html
+        menu:
+        - text: Visium Mouse Kidney
+          href: articles/visium_mouse_kidney.html
+        - text: Visium Mouse Brain
+          href: articles/visium_mouse_brain.html
+        - text: Visium Prostate Integration
+          href: articles/visium_prostate_integration.html
+        - text: CytAssist Human Lung Cancer
+          href: articles/visium_cytassist_lungcancer.html
+        - text: CytAssist Multi-omics Human Glioblastoma
+          href: articles/visium_cytassist_human_glioblastoma.html
       - text: -------
       - text: Spatial Genomics
-      - text: Mouse Kidney
-        href: articles/spatial_genomics_mouse_kidney.html
+        menu:
+        - text: Mouse Kidney
+          href: articles/spatial_genomics_mouse_kidney.html
       - text: -------
       - text: Xenium
-      - text: Xenium Human breast cancer
-        href: articles/xenium_breast_cancer.html
+        menu:
+        - text: Xenium Human breast cancer
+          href: articles/xenium_breast_cancer.html
       - text: -------
       - text: Nanostring CosMx
-      - text: Nanostring CosMx Subcellular Lung Cancer
-        href: articles/nanostring_cosmx_lung_cancer.html
+        menu:
+        - text: Nanostring CosMx Subcellular Lung Cancer
+          href: articles/nanostring_cosmx_lung_cancer.html
       - text: -------
       - text: MERFISH
-      - text: MERFISH Mouse Hypothalamic Preoptic Region
-        href: articles/merfish_mouse_hypothalamic.html
+        menu:
+        - text: MERFISH Mouse Hypothalamic Preoptic Region
+          href: articles/merfish_mouse_hypothalamic.html
       - text: -------
       - text: Vizgen
-      - text: Vizgen Mouse Brain Receptor Map
-        href: articles/vizgen_mouse_brain.html
+        menu:
+        - text: Vizgen Mouse Brain Receptor Map
+          href: articles/vizgen_mouse_brain.html
       - text: -------
       - text: seqFISH
-      - text: mini seqFISH
-        href: articles/mini_seqfish.html
-      - text: SeqFish+ Mouse Cortex Example
-        href: articles/seqfish_cortex.html
+        menu:
+        - text: mini seqFISH
+          href: articles/mini_seqfish.html
+        - text: SeqFish+ Mouse Cortex Example
+          href: articles/seqfish_cortex.html
       - text: -------
       - text: osmFISH
-      - text: osmFISH Mouse SS Cortex
-        href: articles/osmfish_mouse_ss_cortex.html
+        menu:
+        - text: osmFISH Mouse SS Cortex
+          href: articles/osmfish_mouse_ss_cortex.html
       - text: -------
       - text: Resolve Bioscience
-      - text: Resolve Bioscience Breast Cancer Subcellular
-        href: articles/resolve_biosciences.html
+        menu:
+        - text: Resolve Bioscience Breast Cancer Subcellular
+          href: articles/resolve_biosciences.html
       - text: -------
       - text: CODEX
-      - text: Codex Mouse Spleen
-        href: articles/codex_mouse_spleen.html
+        menu:
+        - text: Codex Mouse Spleen
+          href: articles/codex_mouse_spleen.html
       - text: -------
       - text: Single Cell RNA Sequencing
-      - text: Prostate
-        href: articles/singlecell_prostate_standard.html
-      - text: Prostate Integration
-        href: articles/singlecell_prostate_integration.html
+        menu:
+        - text: Prostate
+          href: articles/singlecell_prostate_standard.html
+        - text: Prostate Integration
+          href: articles/singlecell_prostate_integration.html
     news:
       text: News
       menu:
@@ -171,7 +191,10 @@ articles:
   - configuration
   - object_creation
   - structure
+  - errorsfaqsandtips
+  - faqs
   - branches
+  - github_issues
 - title: Try Giotto in the Cloud
   navbar: ~
   contents:

diff --git a/inst/pkgdown/assets/pkgdown.css b/inst/pkgdown/assets/pkgdown.css
@@ -0,0 +1,12 @@
+.dropdown-submenu {
+    height:200px;
+    overflow-y:scroll;
+}
+
+@media (max-width: 500px) {
+    .dropdown-menu{
+        height:200px;
+        overflow-y:scroll;
+    }
+}
+
diff --git a/vignettes/codex_mouse_spleen.Rmd b/vignettes/codex_mouse_spleen.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Codex Mouse Spleen"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Codex Mouse Spleen}

diff --git a/vignettes/configuration.Rmd b/vignettes/configuration.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Giotto Configuration"
-date: 4/12/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Giotto Configuration}

diff --git a/vignettes/ecosystem.Rmd b/vignettes/ecosystem.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Giotto Ecosystem"
-date: 4/12/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Giotto Ecosystem}