Update

-Add dark mode
-Refactor code

.Renviron

@@ -1,4 +1,4 @@
 host = "localhost"
-user = ""
-password = ""
+user = "user"
+password = "pswd"
 port = 3306

functions.R

@@ -22,15 +22,11 @@ with_tooltip <- function(value, tooltip, ...) {
 }
 
 with_tooltip2 <- function(value, tooltip, ...) {
-  #span(style = "text-decoration: underline; text-decoration-style: dotted;", title = tooltip, value)
-  #bsButton("q1", label = tooltip, icon = icon("question"), style = "info", size = "extra-small")
   div(br(),
       tags$style(type = "text/css", "#q1 {vertical-align: top;}"),
       value,
-      #bsButton("tooltipbutton", label = "", icon = icon("question"), style = "info", size = "extra-small"),
       tippy(bsButton("tooltipbutton", label = "", icon = icon("question"), style = "info", size = "extra-small"),
             sprintf("<span style='font-size:15px;'>%s<span>", tooltip), placement = "top", animation = "scale", arrow = TRUE, theme = "blue")
-      #tippy_this("tooltipbutton", sprintf("<span style='font-size:15px;'>%s<span>", tooltip), placement = "top", allowHTML = TRUE, theme = "light")
   )
 }
 
@@ -202,134 +198,6 @@ orange_pal <- function(x){
 }
 
 
-
-# customTheme <- shinyDashboardThemeDIY(
-#   ### general
-#   appFontFamily = "open_sansregular"
-#   ,appFontColor = "rgb(0,0,0)"
-#   ,primaryFontColor = "rgb(0,0,0)"
-#   ,infoFontColor = "rgb(0,0,0)"
-#   ,successFontColor = "rgb(0,0,0)"
-#   ,warningFontColor = "rgb(0,0,0)"
-#   ,dangerFontColor = "rgb(0,0,0)"
-#   ,bodyBackColor = "rgb(248,248,248)"
-#
-#   ### header
-#   ,logoBackColor = "transparent"
-#
-#   ,headerButtonBackColor = "rgb(238,238,238)"
-#   ,headerButtonIconColor = "rgb(75,75,75)"
-#   ,headerButtonBackColorHover = "rgb(210,210,210)"
-#   ,headerButtonIconColorHover = "rgb(0,0,0)"
-#
-#   ,headerBackColor = "rgb(238,238,238)"
-#   ,headerBoxShadowColor = "#aaaaaa"
-#   ,headerBoxShadowSize = "2px 2px 2px"
-#
-#   ### sidebar
-#   ,sidebarBackColor = cssGradientThreeColors(
-#     direction = "down"
-#     ,colorStart = "rgb(20,97,117)"
-#     ,colorMiddle = "rgb(56,161,187)"
-#     ,colorEnd = "rgb(3,22,56)"
-#     ,colorStartPos = 0
-#     ,colorMiddlePos = 50
-#     ,colorEndPos = 100
-#   )
-#   ,sidebarPadding = 0
-#
-#   ,sidebarMenuBackColor = "transparent"
-#   ,sidebarMenuPadding = 0
-#   ,sidebarMenuBorderRadius = 0
-#
-#   ,sidebarShadowRadius = "3px 5px 5px"
-#   ,sidebarShadowColor = "#aaaaaa"
-#
-#   ,sidebarUserTextColor = "rgb(255,255,255)"
-#
-#   ,sidebarSearchBackColor = "rgb(55,72,80)"
-#   ,sidebarSearchIconColor = "rgb(153,153,153)"
-#   ,sidebarSearchBorderColor = "rgb(55,72,80)"
-#
-#   ,sidebarTabTextColor = "rgb(255,255,255)"
-#   ,sidebarTabTextSize = 13
-#   ,sidebarTabBorderStyle = "none none solid none"
-#   ,sidebarTabBorderColor = "rgb(35,106,135)"
-#   ,sidebarTabBorderWidth = 1
-#
-#   ,sidebarTabBackColorSelected = cssGradientThreeColors(
-#     direction = "right"
-#     ,colorStart = "rgba(44,222,235,1)"
-#     ,colorMiddle = "rgba(44,222,235,1)"
-#     ,colorEnd = "rgba(0,255,213,1)"
-#     ,colorStartPos = 0
-#     ,colorMiddlePos = 30
-#     ,colorEndPos = 100
-#   )
-#   ,sidebarTabTextColorSelected = "rgb(0,0,0)"
-#   ,sidebarTabRadiusSelected = "0px 20px 20px 0px"
-#
-#   ,sidebarTabBackColorHover = cssGradientThreeColors(
-#     direction = "right"
-#     ,colorStart = "rgba(44,222,235,1)"
-#     ,colorMiddle = "rgba(44,222,235,1)"
-#     ,colorEnd = "rgba(0,255,213,1)"
-#     ,colorStartPos = 0
-#     ,colorMiddlePos = 30
-#     ,colorEndPos = 100
-#   )
-#   ,sidebarTabTextColorHover = "rgb(50,50,50)"
-#   ,sidebarTabBorderStyleHover = "none none solid none"
-#   ,sidebarTabBorderColorHover = "rgb(75,126,151)"
-#   ,sidebarTabBorderWidthHover = 1
-#   ,sidebarTabRadiusHover = "0px 20px 20px 0px"
-#
-#   ### boxes
-#   ,boxBackColor = "rgb(255,255,255)"
-#   ,boxBorderRadius = 5
-#   ,boxShadowSize = "0px 1px 1px"
-#   ,boxShadowColor = "rgba(0,0,0,.1)"
-#   ,boxTitleSize = 16
-#   ,boxDefaultColor = "rgb(210,214,220)"
-#   ,boxPrimaryColor = "rgba(44,222,235,1)"
-#   ,boxInfoColor = "rgb(210,214,220)"
-#   ,boxSuccessColor = "rgb(210,214,220)"
-#   #,boxSuccessColor = "rgba(0,255,213,1)"
-#   ,boxWarningColor = "rgb(244,156,104)"
-#   ,boxDangerColor = "rgb(255,88,55)"
-#
-#   ,tabBoxTabColor = "rgb(255,255,255)"
-#   ,tabBoxTabTextSize = 14
-#   ,tabBoxTabTextColor = "rgb(0,0,0)"
-#   ,tabBoxTabTextColorSelected = "rgb(0,0,0)"
-#   ,tabBoxBackColor = "rgb(255,255,255)"
-#   ,tabBoxHighlightColor = "rgba(44,222,235,1)"
-#   ,tabBoxBorderRadius = 5
-#
-#   ### inputs
-#   ,buttonBackColor = "rgb(245,245,245)"
-#   ,buttonTextColor = "rgb(0,0,0)"
-#   ,buttonBorderColor = "rgb(200,200,200)"
-#   ,buttonBorderRadius = 5
-#
-#   ,buttonBackColorHover = "rgb(235,235,235)"
-#   ,buttonTextColorHover = "rgb(100,100,100)"
-#   ,buttonBorderColorHover = "rgb(200,200,200)"
-#
-#   ,textboxBackColor = "rgb(255,255,255)"
-#   ,textboxBorderColor = "rgb(200,200,200)"
-#   ,textboxBorderRadius = 5
-#   ,textboxBackColorSelect = "rgb(245,245,245)"
-#   ,textboxBorderColorSelect = "rgb(200,200,200)"
-#
-#   ### tables
-#   ,tableBackColor = "rgb(255,255,255)"
-#   ,tableBorderColor = "rgb(240,240,240)"
-#   ,tableBorderTopSize = 1
-#   ,tableBorderRowSize = 1
-#
-# )
-
 mobileDetect <- function(inputId, value = 0) {
   tagList(
     singleton(tags$head(tags$script(src = "mobile.js"))),

global.R

@@ -13,6 +13,36 @@ source("functions.R")
 
 #rmdfiles <- rmarkdown::render("about.Rmd")
 #sapply(rmdfiles, knitr::knit, quiet = T)
+mouse_orthology<-data.table::fread("./data/HGNC_AllianceHomology.rpt")
+colnames(mouse_orthology)[1:16]<-colnames(mouse_orthology)[2:17]
+mouse_orthology<-mouse_orthology[,-17]
+colnames(mouse_orthology)[2]<-"Gene_name"
+
+mouse_synonyms<-data.table::fread("./data/MRK_List2.rpt")
+colnames(mouse_synonyms)[c(7,12)]<-c("Gene_name","Gene_synonyms")
+mouse_synonyms<-tidyr::separate_rows(mouse_synonyms, Gene_synonyms, sep = "\\|") %>% select(7,12) %>% unique()
+mouse_synonyms<-mouse_synonyms[mouse_synonyms$Gene_synonyms != "",]
+mouse_orthology<-left_join(mouse_orthology, mouse_synonyms, by = "Gene_name")
+
+
+# rbt<-data.frame(Gene_name = rownames(pandora_rabbit))
+# rbt$Gene_name<-str_split(rbt$Gene_name, "\\.", simplify = TRUE)[,1]
+# 
+# rbt$Gene_name2<-mouse_orthology$`HGNC ID`[match(rbt$Gene_name, mouse_orthology$Gene_name)]
+# rbt$Gene_name3<-mouse_orthology$`HGNC ID`[match(rbt$Gene_name, mouse_orthology$Gene_synonyms)]
+# rbt$Gene_name2<-with(rbt, ifelse(is.na(Gene_name2), Gene_name3, Gene_name2))
+# rbt$Gene_name2<-with(rbt, ifelse(is.na(Gene_name2), Gene_name, Gene_name2))
+
+
+hgnc_names<-fread("./data/hgnc_names.txt") %>% filter(Status == "Approved") %>% dplyr::select(1,3)
+mouse_orthology2<-tidyr::separate_rows(mouse_orthology, `HGNC ID`, sep = "\\|")
+mouse_orthology2<-mouse_orthology2[,c(1,2,5,10,16,17)]
+mouse_orthology2<-left_join(mouse_orthology2, hgnc_names, by = "HGNC ID")
+
+
+# pandora_rabbit_full<-readRDS("./data/sc_data/12_Rabbit_Lung.rds")
+# data_to_write_out <- as.data.frame(as.matrix(pandora_rabbit_full@assays$RNA@data))
+# fwrite(x = data_to_write_out, row.names = TRUE, file = "rabbit.csv")
 
 lung<-readRDS("./data/lung_reduced.RDS")
 #lung<-readRDS(url("https://drive.google.com/uc?export=download&id=1Q9WKkQml3woMnvvHPj_whj9O37a5cMjF","rb"))
@@ -30,12 +60,36 @@ habermann<-readRDS("./data/banovich_reduced.RDS")
 habermann_markers<-fread("./data/banovich_markers.txt") %>%
   relocate(gene, .before = p_val)
 
+pandora_tiger<-readRDS("./data/sc_data/tiger_reduced.rds")
+pandora_pangolin<-readRDS("./data/sc_data/pangolin_reduced.rds")
+pandora_deer<-readRDS("./data/sc_data/deer_reduced.rds")
+pandora_goat<-readRDS("./data/sc_data/goat_reduced.rds")
+pandora_rabbit<-readRDS("./data/sc_data/rabbit_reduced.rds")
+pandora_cat<-readRDS("./data/sc_data/cat_reduced.rds")
+pandora_dog<-readRDS("./data/sc_data/dog_reduced.rds")
+pandora_hamster<-readRDS("./data/sc_data/hamster_reduced.rds")
+pandora_lizard<-readRDS("./data/sc_data/lizard_reduced.rds")
+pandora_duck<-readRDS("./data/sc_data/duck_reduced.rds")
+pandora_pigeon<-readRDS("./data/sc_data/pigeon_reduced.rds")
+pandora_bat<-readRDS("./data/sc_data/bat_reduced.rds")
+
+
 cele<-readRDS("./data/cele_seurat.RDS")
+
+pandora.list<-data.frame(paper = c("Tiger Lung","Pangolin Lung","Deer Lung","Goat Lung","Rabbit Lung","Cat Lung",
+                                   "Dog Lung","Hamster Lung","Lizard Lung","Duck Lung","Pigeon Lung","Bat Lung"),
+                         data = c("pandora_tiger","pandora_pangolin","pandora_deer","pandora_goat","pandora_rabbit",
+                                  "pandora_cat","pandora_dog","pandora_hamster","pandora_lizard","pandora_duck",
+                                  "pandora_pigeon","pandora_bat"))
+
 sc.paper.list<-data.frame(paper = c("Carraro et al(2021) - Lung (human)",
                                     "Reyfman et al(2018) - Lung (human)",
                                     "Habermann et al(2020) - Lung (human)",
+                                    "Chen et al(2021) - Lung(mammals, reptiles, birds)",
                                     "Cao et al(2017) - C. elegans"),
-                          data = c("lung","reyfman","habermann","cele"))
+                          data = c("lung","reyfman","habermann","pandora.list","cele"))
+
+
 lung_names<-rownames(lung)
 reyfman_names<-rownames(reyfman)
 habermann_names<-rownames(habermann)
@@ -65,6 +119,10 @@ homsap<-tbl(db, "gene_info_edited") %>%
   collect()
 orthology<-tbl(db, "orthology") %>%
   collect()
+orthology<-hgncConverter(orthology, "Gene2Symbol")
+colnames(orthology)[1]<-"Gene_name"
+orthology<-semi_join(orthology, homsap, by = "Gene_name")
+colnames(orthology)[1]<-"Gene2Symbol"
 dbDisconnect(db)
 
 ciliogenics<-final_score_table %>%

modules/module1.R

@@ -0,0 +1,18 @@
+
+
+geneinfo_ui <- function(id){
+  ns <- NS(id)
+  uiOutput(ns("geneinfo"))
+}
+
+geneinfo_server <- function(id, genename){
+  moduleServer(
+    id,
+    function(input, output, session){
+      output$geneinfo <- renderUI({
+        ns <- session$ns
+        HTML(paste("The data shown are for", '<b style="color:#edbc40">', genename(),'</b>', "gene"))
+      })
+    }
+  )
+}