update link icons

rnabioco · Feb 25, 2024 · b5c9d52 · b5c9d52
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diff --git a/atlases/2021-carpentier-34618370/index.qmd b/atlases/2021-carpentier-34618370/index.qmd
@@ -2,7 +2,7 @@
 title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination
 
 image: /images/2021-carpentier-34618370.jpg
-subtitle: '[Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
+subtitle: '[<i class="bi bi-compass"></i> Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
 date: 'November 15, 2021'
 categories: [Project-1, Project-2, Core-C, Core-D, 2021]
 about:

diff --git a/atlases/2021-walsh-33843587/index.qmd b/atlases/2021-walsh-33843587/index.qmd
@@ -2,7 +2,7 @@
 title: Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node
 
 image: /images/2021-walsh-33843587.jpg
-subtitle: '[Atlas](https://d3898ys7yh3545.cloudfront.net/){.link-box-large}'
+subtitle: '[<i class="bi bi-compass"></i> Atlas](https://d3898ys7yh3545.cloudfront.net/){.link-box-large}'
 date: 'April 12, 2021'
 categories: [Project-2, Core-C, Core-D, 2021]
 about:

diff --git a/atlases/2024-lucas-38194268/index.qmd b/atlases/2024-lucas-38194268/index.qmd
@@ -1,7 +1,7 @@
 ---
 title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
 
-subtitle: '[Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
+subtitle: '[<i class="bi bi-compass"></i> Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
 date: 'January 09, 2024'
 categories: [Project-1, Project-2, Core-C, Core-D, 2024]
 about:

diff --git a/funs.R b/funs.R
@@ -1,4 +1,4 @@
-#' Create links for a project
+#' Create links for a project section
 #' 
 #' links to atlases, publications, investigators
 .create_project_links <- function(proj_yml, athr_yml, pub_yml, lnk_cls) {
@@ -34,7 +34,8 @@
 
       if (any(pubs)) {
         lnks <- str_c(
-          lnks, " [Publications](pubs.qmd#category=", proj_lnk, ")",
+          lnks, " [<i class='bi bi-file-earmark'></i> Publications]",
+          "(pubs.qmd#category=", proj_lnk, ")",
           lnk_cls
         )
       }
@@ -45,7 +46,8 @@
 
       if (any(atlases)) {
         lnks <- str_c(
-          lnks, " [Atlases](atlases.qmd#category=", proj_lnk, ")",
+          lnks, " [<i class='bi bi-compass'></i> Atlases]",
+          "(atlases.qmd#category=", proj_lnk, ")",
           lnk_cls
         )
       }
@@ -60,17 +62,45 @@
 #' 
 #' links to the project page
 .create_project_link <- function(proj_title, lnk_name = proj_title,
-                                 lnk_cls = "{.link-bold}", max_len = 64) {
+                                 lnk_cls = "{.link-bold}", max_len = 40,
+                                 return_id = FALSE) {
   res <- proj_title %>%
     str_to_lower() %>%
     str_replace_all("( |, )", "-") %>%
     str_trunc(max_len, "right", ellipsis = "") %>%
-    str_remove("-$") %>%
+    str_remove("-$")
+
+  if (return_id) return(res)
+
+  res <- res %>%
     str_c("[", lnk_name, "](projects.qmd#", ., ")", lnk_cls)
 
   res
 }
 
+#' Add icon to link
+.icon_key <- list(
+  publications = "bi bi-file-earmark",
+  atlases      = "bi bi-compass",
+  atlas        = "bi bi-compass",
+  email        = "bi bi-envelope",
+  website      = "bi bi-house"
+  # website      = "bi bi-globe"
+)
+
+.add_link_icon <- function(lnk_text, icon_key = .icon_key) {
+
+  icon <- .icon_key[[lnk_text]]
+
+  if (!is.null(icon)) icon <- str_c("<i class='", icon, "'></i> ")
+
+  res <- lnk_text %>%
+    str_to_title() %>%
+    str_c("[", icon, ., "]")
+
+  res  
+}
+
 #' Create publication page
 #' 
 #' * Check publication information and scrape missing information from pubmed
@@ -133,9 +163,10 @@
       return(NULL)
     }
 
-    subttl <- links %>%
-      pluck("atlas") %>%
-      str_c("[Atlas](", ., "){.link-box-large}")
+    subttl <- links %>%   # use double quotes single subtitle will be wrapped
+      pluck("atlas") %>%  # in single quotes
+      str_c(.add_link_icon("atlas"), "(", ., "){.link-box-large}") %>%
+      str_replace_all("'", "\\\"")
 
     links <- links[names(links) != "atlas"]
   }

diff --git a/investigators.qmd b/investigators.qmd
@@ -1,6 +1,5 @@
 ---
 title: "Investigators"
-toc: true
 ---
 
 ```{r, echo = FALSE, include = FALSE}
@@ -29,12 +28,13 @@ proj_lnks <- proj_yml %>%
   imap(~ .create_project_link(.x$title, str_to_title(.y), "{.link-box-fade}"))
 
 # Create page text
+# unable to include table of contents and have the image inline with heading
 text <- athr_yml %>%
   imap(~ {
     lnks <- .x$links %>%  # links to project pages
-      imap(~ str_c("[", str_to_title(.y), "](", .x, ")", lnk_cls)) %>%
+      imap(~ str_c(.add_link_icon(.y), "(", .x, ")", lnk_cls)) %>%
       str_c(collapse = " ")
-    
+
     lnks <- proj_lnks[.x$project] %>%
       str_c(collapse = " ") %>%
       str_c(lnks, " ", .)
@@ -45,8 +45,8 @@ text <- athr_yml %>%
     
     res <- str_c(
       "<h2>", .y, sfx, "</h2>\n\n",
-      lnks,           "\n\n",
-      .x$bio,         "\n\n"
+      lnks, "\n\n",
+      .x$bio, "\n\n"
     )
     
     # Add image for each investigator
@@ -58,12 +58,7 @@ text <- athr_yml %>%
         "  <img src='", img, "'>\n"
       )
       
-      html_foot <- "</div>"
-      
-      res <- str_c(
-        html_head, res,
-        html_foot, "\n\n"
-      )
+      res <- str_c(html_head, res, "</div>\n\n")
     }
     
     res

diff --git a/pre-build.R b/pre-build.R
@@ -124,9 +124,13 @@ tl_dat <- tl_dat %>%
   mutate(
     pmid = str_remove(pmid, "/$"),
     pmid = str_c("PMID", pmid),
-    lab  = str_c(proj, "\n", pmid),
     year = as.character(year(date)),
     url  = file.path(pub_dir, key)
+  ) %>%
+  pivot_longer(c(proj, pmid), values_to = "lab") %>%
+  mutate(
+    style = ifelse(name == "pmid", "bold", "normal"),
+    style = map(style, ~ list(`font-weight` = .x))
   )
 
 # Save as json file

diff --git a/projects.qmd b/projects.qmd
@@ -6,7 +6,6 @@ toc: true
 library(yaml)
 library(tidyverse)
 library(here)
-
 source(here("funs.R"))
 
 # Read yamls
@@ -39,10 +38,15 @@ text <- proj_yml %>%
         # Conditional add hypothesis
         hyp <- .x$hypothesis
         
-        if (!is.null(hyp)) hyp <- str_c("*", hyp, "*\n\n")
+        if (!is.null(hyp)) hyp <- str_c("<i>", hyp, "</i>\n\n")
+        
+        # Set heading IDs
+        # need this since the first h2 heading ID after h1 gets mixed up during
+        # rendering
+        id <- .create_project_link(.x$title, return_id = TRUE)
         
         res <- str_c(
-          "<h2>", .x$title, "</h2>\n\n",
+          "<h2 id=", id, ">", .x$title, "</h2>\n\n",
           links[[.y]], "\n\n",
           hyp
         )
@@ -65,7 +69,7 @@ text <- proj_yml %>%
           body <- str_c(
             "<div class='project-image'>\n",
             "  <img src='", img, "'>\n",
-            body, "\n\n",
+            body, "\n",
             "</div>"
           )
         }

diff --git a/pubs.qmd b/pubs.qmd
@@ -39,7 +39,8 @@ file.copy("timeline.json", "_site")
                 .mapping({
                     'timestamp': 'year',
                     'text': 'lab',
-                    'url': 'url'
+                    'url': 'url',
+                    'textStyle': 'style'
                 })
                 .parseTime('%Y')
                 .aggregateBy('year')

diff --git a/theme.scss b/theme.scss
@@ -55,12 +55,12 @@ div.sidebar-item-container .active, div.sidebar-item-container .show>.nav-link,
 }
 
 .link-box-large {
-  display:         inline-block;   // Ensures the box wraps the content 
-  text-decoration: none;           // Removes the underline from the link
+  display:         inline-block;      // Ensures the box wraps the content 
+  text-decoration: none;              // Removes the underline from the link
   color:           $link-color;
   border:          1px solid $link-color;
-  border-radius:   5px;            // Rounded corners; adjust radius as needed
-  padding:         0px 8px;        // Padding inside box around the text
+  border-radius:   7px;               // Rounded corners; adjust radius as needed
+  padding:         0.125rem 0.25rem;  // Padding inside box around the text
   margin:          1.5px;
   margin-top:      5px;
   margin-bottom:   5px;
@@ -74,6 +74,7 @@ div.sidebar-item-container .active, div.sidebar-item-container .show>.nav-link,
 .link-box { 
   @extend .link-box-large;
   font-size: 0.8rem;
+  border-radius: 0.25rem;
 }
 
 .link-box-fade {
@@ -153,7 +154,7 @@ p.subtitle {
 
 // Timeline
 #timeline {
-  margin-right:  80px;
+  margin-right:  100px;
   margin-bottom: 50px;
 }
 
@@ -180,5 +181,5 @@ p.subtitle {
 
 .milestones-label.milestones-link-label {
   @extend .link-bw;
-  font-size: 0.75rem !important;
+  font-size: 0.65rem !important;
 }
diff --git a/timeline.json b/timeline.json
@@ -1 +1 @@
-[{"key":"2021-walsh-33843587","date":"2021-01-01","proj":"Project-2, Core-C, Core-D","authors":"Sheridan, Hesselberth, Tamburini","pmid":"PMID33843587","lab":"Project-2, Core-C, Core-D\nPMID33843587","year":"2021","url":"pubs/2021-walsh-33843587"},{"key":"2017-kedl-29229919","date":"2017-01-01","proj":"Project-2","authors":"Tamburini","pmid":"PMID29229919","lab":"Project-2\nPMID29229919","year":"2017","url":"pubs/2017-kedl-29229919"},{"key":"2021-carpentier-34618370","date":"2021-01-01","proj":"Project-1, Project-2, Core-C, Core-D","authors":"Sheridan, Tamburini, Hesselberth, Morrison","pmid":"PMID34618370","lab":"Project-1, Project-2, Core-C, Core-D\nPMID34618370","year":"2021","url":"pubs/2021-carpentier-34618370"},{"key":"2022-doan-35505125","date":"2022-01-01","proj":"Project-2","authors":"Tamburini","pmid":"PMID35505125","lab":"Project-2\nPMID35505125","year":"2022","url":"pubs/2022-doan-35505125"},{"key":"2024-lucas-38194268","date":"2024-01-01","proj":"Project-1, Project-2, Core-C, Core-D","authors":"Sheridan, Hesselberth, Tamburini, Morrison","pmid":"PMID38194268","lab":"Project-1, Project-2, Core-C, Core-D\nPMID38194268","year":"2024","url":"pubs/2024-lucas-38194268"},{"key":"2018-mccarthy-29997290","date":"2018-01-01","proj":"Project-1, Project-2","authors":"Tamburini, Morrison","pmid":"PMID29997290","lab":"Project-1, Project-2\nPMID29997290","year":"2018","url":"pubs/2018-mccarthy-29997290"},{"key":"2018-lucas-30045970","date":"2018-01-01","proj":"Project-1, Project-2","authors":"Morrison, Tamburini","pmid":"PMID30045970","lab":"Project-1, Project-2\nPMID30045970","year":"2018","url":"pubs/2018-lucas-30045970"},{"key":"2019-tamburini-31156626","date":"2019-01-01","proj":"Project-2, Core-C, Core-D","authors":"Tamburini, Hesselberth","pmid":"PMID31156626","lab":"Project-2, Core-C, Core-D\nPMID31156626","year":"2019","url":"pubs/2019-tamburini-31156626"},{"key":"2020-lucas-33053342","date":"2020-01-01","proj":"Project-2, Core-B","authors":"Matsuda, Tamburini","pmid":"PMID33053342","lab":"Project-2, Core-B\nPMID33053342","year":"2020","url":"pubs/2020-lucas-33053342"},{"key":"2023-tamburini-37841845","date":"2023-01-01","proj":"Project-1, Project-2, Core-C, Core-D","authors":"Tamburini, Hesselberth, Morrison","pmid":"PMID37841845","lab":"Project-1, Project-2, Core-C, Core-D\nPMID37841845","year":"2023","url":"pubs/2023-tamburini-37841845"},{"key":"2024-kim-38307020","date":"2024-01-01","proj":"Project-1, Core-B","authors":"Morrison, Matsuda","pmid":"PMID38307020","lab":"Project-1, Core-B\nPMID38307020","year":"2024","url":"pubs/2024-kim-38307020"},{"key":"2014-tamburini-24905362","date":"2014-01-01","proj":"Project-2","authors":"Tamburini","pmid":"PMID24905362","lab":"Project-2\nPMID24905362","year":"2014","url":"pubs/2014-tamburini-24905362"}]
+[{"key":"2021-walsh-33843587","date":"2021-01-01","authors":"Sheridan, Hesselberth, Tamburini","year":"2021","url":"pubs/2021-walsh-33843587","name":"proj","lab":"Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2021-walsh-33843587","date":"2021-01-01","authors":"Sheridan, Hesselberth, Tamburini","year":"2021","url":"pubs/2021-walsh-33843587","name":"pmid","lab":"PMID33843587","style":{"font-weight":["bold"]}},{"key":"2017-kedl-29229919","date":"2017-01-01","authors":"Tamburini","year":"2017","url":"pubs/2017-kedl-29229919","name":"proj","lab":"Project-2","style":{"font-weight":["normal"]}},{"key":"2017-kedl-29229919","date":"2017-01-01","authors":"Tamburini","year":"2017","url":"pubs/2017-kedl-29229919","name":"pmid","lab":"PMID29229919","style":{"font-weight":["bold"]}},{"key":"2021-carpentier-34618370","date":"2021-01-01","authors":"Sheridan, Tamburini, Hesselberth, Morrison","year":"2021","url":"pubs/2021-carpentier-34618370","name":"proj","lab":"Project-1, Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2021-carpentier-34618370","date":"2021-01-01","authors":"Sheridan, Tamburini, Hesselberth, Morrison","year":"2021","url":"pubs/2021-carpentier-34618370","name":"pmid","lab":"PMID34618370","style":{"font-weight":["bold"]}},{"key":"2022-doan-35505125","date":"2022-01-01","authors":"Tamburini","year":"2022","url":"pubs/2022-doan-35505125","name":"proj","lab":"Project-2","style":{"font-weight":["normal"]}},{"key":"2022-doan-35505125","date":"2022-01-01","authors":"Tamburini","year":"2022","url":"pubs/2022-doan-35505125","name":"pmid","lab":"PMID35505125","style":{"font-weight":["bold"]}},{"key":"2024-lucas-38194268","date":"2024-01-01","authors":"Sheridan, Hesselberth, Tamburini, Morrison","year":"2024","url":"pubs/2024-lucas-38194268","name":"proj","lab":"Project-1, Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2024-lucas-38194268","date":"2024-01-01","authors":"Sheridan, Hesselberth, Tamburini, Morrison","year":"2024","url":"pubs/2024-lucas-38194268","name":"pmid","lab":"PMID38194268","style":{"font-weight":["bold"]}},{"key":"2018-mccarthy-29997290","date":"2018-01-01","authors":"Tamburini, Morrison","year":"2018","url":"pubs/2018-mccarthy-29997290","name":"proj","lab":"Project-1, Project-2","style":{"font-weight":["normal"]}},{"key":"2018-mccarthy-29997290","date":"2018-01-01","authors":"Tamburini, Morrison","year":"2018","url":"pubs/2018-mccarthy-29997290","name":"pmid","lab":"PMID29997290","style":{"font-weight":["bold"]}},{"key":"2018-lucas-30045970","date":"2018-01-01","authors":"Morrison, Tamburini","year":"2018","url":"pubs/2018-lucas-30045970","name":"proj","lab":"Project-1, Project-2","style":{"font-weight":["normal"]}},{"key":"2018-lucas-30045970","date":"2018-01-01","authors":"Morrison, Tamburini","year":"2018","url":"pubs/2018-lucas-30045970","name":"pmid","lab":"PMID30045970","style":{"font-weight":["bold"]}},{"key":"2019-tamburini-31156626","date":"2019-01-01","authors":"Tamburini, Hesselberth","year":"2019","url":"pubs/2019-tamburini-31156626","name":"proj","lab":"Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2019-tamburini-31156626","date":"2019-01-01","authors":"Tamburini, Hesselberth","year":"2019","url":"pubs/2019-tamburini-31156626","name":"pmid","lab":"PMID31156626","style":{"font-weight":["bold"]}},{"key":"2020-lucas-33053342","date":"2020-01-01","authors":"Matsuda, Tamburini","year":"2020","url":"pubs/2020-lucas-33053342","name":"proj","lab":"Project-2, Core-B","style":{"font-weight":["normal"]}},{"key":"2020-lucas-33053342","date":"2020-01-01","authors":"Matsuda, Tamburini","year":"2020","url":"pubs/2020-lucas-33053342","name":"pmid","lab":"PMID33053342","style":{"font-weight":["bold"]}},{"key":"2023-tamburini-37841845","date":"2023-01-01","authors":"Tamburini, Hesselberth, Morrison","year":"2023","url":"pubs/2023-tamburini-37841845","name":"proj","lab":"Project-1, Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2023-tamburini-37841845","date":"2023-01-01","authors":"Tamburini, Hesselberth, Morrison","year":"2023","url":"pubs/2023-tamburini-37841845","name":"pmid","lab":"PMID37841845","style":{"font-weight":["bold"]}},{"key":"2024-kim-38307020","date":"2024-01-01","authors":"Morrison, Matsuda","year":"2024","url":"pubs/2024-kim-38307020","name":"proj","lab":"Project-1, Core-B","style":{"font-weight":["normal"]}},{"key":"2024-kim-38307020","date":"2024-01-01","authors":"Morrison, Matsuda","year":"2024","url":"pubs/2024-kim-38307020","name":"pmid","lab":"PMID38307020","style":{"font-weight":["bold"]}},{"key":"2014-tamburini-24905362","date":"2014-01-01","authors":"Tamburini","year":"2014","url":"pubs/2014-tamburini-24905362","name":"proj","lab":"Project-2","style":{"font-weight":["normal"]}},{"key":"2014-tamburini-24905362","date":"2014-01-01","authors":"Tamburini","year":"2014","url":"pubs/2014-tamburini-24905362","name":"pmid","lab":"PMID24905362","style":{"font-weight":["bold"]}}]
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
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		[{"key":"2021-walsh-33843587","date":"2021-01-01","authors":"Sheridan, Hesselberth, Tamburini","year":"2021","url":"pubs/2021-walsh-33843587","name":"proj","lab":"Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2021-walsh-33843587","date":"2021-01-01","authors":"Sheridan, Hesselberth, Tamburini","year":"2021","url":"pubs/2021-walsh-33843587","name":"pmid","lab":"PMID33843587","style":{"font-weight":["bold"]}},{"key":"2017-kedl-29229919","date":"2017-01-01","authors":"Tamburini","year":"2017","url":"pubs/2017-kedl-29229919","name":"proj","lab":"Project-2","style":{"font-weight":["normal"]}},{"key":"2017-kedl-29229919","date":"2017-01-01","authors":"Tamburini","year":"2017","url":"pubs/2017-kedl-29229919","name":"pmid","lab":"PMID29229919","style":{"font-weight":["bold"]}},{"key":"2021-carpentier-34618370","date":"2021-01-01","authors":"Sheridan, Tamburini, Hesselberth, Morrison","year":"2021","url":"pubs/2021-carpentier-34618370","name":"proj","lab":"Project-1, 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