Merge pull request #5 from rnabioco/site-updates

Site updates

_quarto.yml

@@ -28,5 +28,5 @@ format:
     toc: true
     toc-depth: 1
 
-editor: visual
+editor: source
 

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:

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:

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:

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"]
   }

index.qmd

@@ -47,11 +47,21 @@ text <- proj_yml %>%
     .x %>%
       imap(~ {
         ttl_lnk <- .create_project_link(.x$title)
+        
+        proj_tag <- .y %>%
+          str_replace_all("-", " ") %>%
+          str_to_title()
+        
+        bld_tag <- proj_tag %>%
+          str_c("<span class='text-bold'>", ., "</span>")
+          
+        body <- .x$short %>%
+          str_replace(proj_tag, bld_tag)
       
         str_c(
           "* ", ttl_lnk, "  \n",
           links[[.y]],   "  \n",
-          .x$short,      "\n\n"
+          body,          "\n\n"
         )
       }) %>%
       str_c(collapse = "") %>%

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

pre-build.R

@@ -113,6 +113,7 @@ tl_dat <- pub_yml_new %>%
     tibble(
       key     = .x$key,
       date    = as.Date(str_c(.x$year, "-01-01")),
+      proj    = str_c(str_to_title(.x$project), collapse = ", "),
       authors = str_c(athrs, collapse = ", "),
       pmid    = str_extract(.x$pubmed, "[0-9]+(/|)$")
     )
@@ -123,9 +124,13 @@ tl_dat <- tl_dat %>%
   mutate(
     pmid = str_remove(pmid, "/$"),
     pmid = str_c("PMID", pmid),
-    lab  = str_c(authors, "\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

projects.qmd

@@ -6,7 +6,6 @@ toc: true
 library(yaml)
 library(tidyverse)
 library(here)
-
 source(here("funs.R"))
 
 # Read yamls
@@ -39,15 +38,29 @@ 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
         )
         
-        body <- .x$abstract
+        # Bold project tag (e.g. project-1)
+        proj_tag <- .y %>%
+          str_replace_all("-", " ") %>%
+          str_to_title()
+        
+        bld_tag <- proj_tag %>%
+          str_c("<span class='text-bold'>", ., "</span>")
+          
+        body <- .x$abstract %>%
+          str_replace(proj_tag, bld_tag)
         
         # Add image for each project
         if (!is.null(.x$image)) {
@@ -56,7 +69,7 @@ text <- proj_yml %>%
           body <- str_c(
             "<div class='project-image'>\n",
             "  <img src='", img, "'>\n",
-            .x$abstract, "\n\n",
+            body, "\n",
             "</div>"
           )
         }

projects.yml

@@ -1,58 +1,58 @@
 project-1:
   title: Define protective and pathogenic roles of LNSCs during viral infection
-  short: Project 1 will define how viral targeting of distinct LNSCs regulates
+  short: "Project 1 will define how viral targeting of distinct LNSCs regulates
     viral dissemination, LN organization and inflammation, and development of
-    adaptive immunity
+    adaptive immunity"
   hypothesis: We hypothesize that inflammatory responses, cell trafficking, and
     development of protective adaptive immune responses are regulated by
     discrete populations of LNSCs during viral infection
   image: /images/project-1.png
-  abstract: Project 1 will define how viral targeting of distinct LNSCs
+  abstract: "Project 1 will define how viral targeting of distinct LNSCs
     regulates viral dissemination, LN organization and inflammation, and
-    development of adaptive immunity. Project 1 and Project 2 will establish
+    development of adaptive immunity. Project 1 will establish
     how viral targeting of LNSCs impacts antigen archiving and immune memory to
-    archived antigens. Finally, Project 1 coordinates with Project 3 to study
+    archived antigens. Finally, Project 1 will study
     how isotype-specific immune complexes (ICs) promote chronic viral infection
     of follicular dendritic cells (FDCs).
     This project will use novel mouse models and human tissues and advanced
     spatial and single-cell RNA approaches. This project will define how LNSCs
     shape antiviral immune responses and how viruses manipulate LNSCs to evade
-    immunity.
+    immunity."
 
 project-2:
   title: Identify mechanisms of vaccine antigen localization and retention by
     LNSCs that drive and enhance cellular and humoral immunity
-  short: Project 2 will define mechanisms of vaccine antigen acquisition and
-    retention by different LNSCs
+  short: "Project 2 will define mechanisms of vaccine antigen acquisition and
+    retention by different LNSCs"
   hypothesis: We hypothesize that LNSC targeting improves and extends the
     cellular and humoral responses required for vaccine mediated immunity
   image: /images/project-2.png
-  abstract: Project 2 will work with Project 3 to define mechanisms of vaccine
-    antigen acquisition and retention by different LNSCs. Project 2 will work
-    with Projects 1 and 3 to determine if manipulation of antigen duration in
+  abstract: "Project 2 will define mechanisms of vaccine
+    antigen acquisition and retention by different LNSCs. Project 2 will
+    determine if manipulation of antigen duration in
     LNSCs improves vaccine protection against arboviruses and influenza virus.
-    Finally, Project 2 will work with Project 1 to define the consequences of
-    virus induced cell death on LEC "training" and the impact on vaccine
+    Finally, Project 2 will define the consequences of
+    virus induced cell death on LEC 'training' and the impact on vaccine
     immunity.
     This project will distinguish functions of specific LNSC populations and
     create novel vaccine strategies (e.g., mRNA, virus-like particles, and
     lipid nanoparticles) and apply sophisticated spatial and single-cell
     transcriptomic approaches to evaluate antigen levels within infrequent and
     transcriptionally defined LNSC subsets. This project will determine how
     specific LNSC subsets shape vaccine immunity and the consequences of viral
-    infection of LNSCs to vaccine immunity.
+    infection of LNSCs to vaccine immunity."
 
 project-3:
   title: Investigate the role of immune complexes in antigen acquisition and
     retention by LNSCs to modulate cellular and humoral immunity
-  short: Project 3 will use stabilized DNA conjugates to track antibody:antigen
+  short: "Project 3 will use stabilized DNA conjugates to track antibody:antigen
     complexes to determine the spatial and cellular localization of immune
-    complexes
+    complexes"
   hypothesis: We hypothesize that antibody isotype in an IC regulates protective
     immunity by determining which LNSC populations acquire and retain antigen
     via isotype-specific interactions with complement and Fc receptors (FcRs)
   image: /images/project-3.png
-  abstract: Project 3 will engineer monoclonal antibodies (mAbs) with fixed
+  abstract: "Project 3 will engineer monoclonal antibodies (mAbs) with fixed
     antigen specificity on discrete antibody isotypes and subclasses. Using
     stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen
     complexes to determine the spatial and cellular localization of ICs in
@@ -62,27 +62,27 @@ project-3:
     cellular immunity. This project will use mouse models engineered to
     manipulate complement receptor and FcR expression by discrete LNSC
     populations and will define how different LNSC populations use antibody to
-    determine antigen uptake and localization.
+    determine antigen uptake and localization."
 
 core-b:
   title: Mouse transgenics and tissue characterization
-  short: The goal of the animal and tissue core is to generate novel genetic
-    mouse models and to develop a tissue and cell repository
-  abstract: "The goal of the mouse transgenics and tissue core is to generate
-    novel genetic mouse models and to develop a tissue and cell repository, this
-    includes the following key tasks.\n\n
+  short: "Core B will generate novel genetic
+    mouse models and develop a tissue and cell repository"
+  abstract: "Core B will generate
+    novel genetic mouse models and develop a tissue and cell repository, this
+    includes the following tasks.\n\n
     **Task 1.** Generation of novel mouse lines\n\n
     **Task 2.** Provide a mouse colony for LNSC biology\n\n
     **Task 3.** Provide a resource for maintenance and distribution of human and
     mouse LNSCs and lymphoid tissues"
 
 core-c:
   title: Molecular technologies
-  short: The molecular technologies core will apply new molecular tools to
-    understand the contributions of lymph node stromal cells to immune responses
-  abstract: "The molecular technologies cores will apply new molecular tools to
+  short: "Core C will apply new molecular tools to
+    understand the contributions of lymph node stromal cells to immune responses"
+  abstract: "Core C will apply new molecular tools to
     understand the contributions of lymph node stromal cells to immune
-    responses, this includes the following key tasks.\n\n
+    responses, this includes the following tasks.\n\n
     **Task 1.** Generate validated reagents for and execute single-cell and
     spatial transcriptomic experiments to probe LNSC biology\n\n
     **Task 2.** Production of customized lipid nanoparticles with mRNA and siRNA
@@ -92,9 +92,9 @@ core-c:
 
 core-d:
   title: Bioinformatics
-  short: The bioinformatics core will apply new informatics approaches to
-    understand the contributions of lymph node stromal cells (LN    SC) to immune responses
-  abstract: "The bioinformatics core will apply new informatics approaches to
+  short: "Core D will apply new informatics approaches to
+    understand the contributions of LNSCs to immune responses"
+  abstract: "Core D will apply new informatics approaches to
     understand the contributions of LNSCs to immune responses, this includes the
     following tasks.\n\n
     **Task 1.** Provide a bioinformatics resource for rigorous and reproducible