Update PFCapp.qmd

PFCapp.qmd

@@ -4,7 +4,7 @@ author: "Cao Lab"
 server: shiny
 format: 
   dashboard:
-    logo: https://zhenghu159.github.io/picx-images-hosting/PFCapp/Logo.1756dx3zx7.webp
+    logo: https://zhenghu159.github.io/picx-images-hosting/PFCapp/Logo-circle.7sn4nqapcl.png
     nav-buttons:
       - icon: github
         href: https://github.com/GangCaoLab/mPFC-web
@@ -319,6 +319,8 @@ output$sp_gene_plot <- renderPlot({
     Zscore = scale(log1p(sp.PFC@assays$RNA@counts[input$sp_gene,]))
     )
   df <- df[which(sp.PFC$slice==input$sp_slice),]
+  df$Zscore[df$Zscore<0] <- 0
+  df$Zscore[df$Zscore>3] <- 3
   df <- df[order(df$Zscore),]
   ggplot(df,aes(x=X,y=Y)) +
     geom_point(aes(colour=Zscore), size=1) +
@@ -332,13 +334,18 @@ output$sp_gene_plot <- renderPlot({
 
 output$sp_target_plot <- renderPlot({
   seu <- sp.PFC
-  seu@meta.data[,c("PTi","ITi_D","ITi_V","ITc")][is.na(seu@meta.data[,c("PTi","ITi_D","ITi_V","ITc")])] <- 0
+  seu$PTi[is.na(seu$PTi)] <- 0
+  seu$ITi_D[is.na(seu$ITi_D)] <- 0
+  seu$ITi_V[is.na(seu$ITi_V)] <- 0
+  seu$ITc[is.na(seu$ITc)] <- 0
   df <- data.frame(
-    X = sp.PFC$ML_new,
-    Y = sp.PFC$DV_new,
-    Zscore = scale(log1p(sp.PFC@meta.data[,input$sp_target]))
+    X = seu$ML_new,
+    Y = seu$DV_new,
+    Zscore = scale(log1p(seu@meta.data[,input$sp_target]))
   )
-  df <- df[which(sp.PFC$slice==input$sp_slice),]
+  df <- df[which(seu$slice==input$sp_slice),]
+  df$Zscore[df$Zscore<0] <- 0
+  df$Zscore[df$Zscore>3] <- 3
   df <- df[order(df$Zscore),]
   ggplot(df, aes(x=X,y=Y)) +
     geom_point(aes(colour=Zscore), size=1) +
@@ -413,7 +420,13 @@ output$sp_target_line_plot <- renderPlot({
 ## {.sidebar}
 
 ```{r}
-selectInput('subtype', 'Select SubType', sort(unique(sp.PFC$SubType)))
+sp_Barcode <- c("ITi-D", "ITi-V", "ITc", "PTi",
+                'VIS-I','SSp-I','CP-I','AUD-I','RSP-I',
+                'BLA-I','ACB-I','AId-I','ECT-I',
+                'ACB-C','ECT-C','CP-C','AId-C','RSP-C',
+                'LHA-I')
+selectInput('subtype_3d', 'Select SubType', sort(unique(sp.PFC$SubType)))
+selectInput('target_3d', 'Select Target', sp_Barcode)
 ```
 
 
@@ -427,42 +440,58 @@ rglwidgetOutput('spatial_subtype', width = "100%")
 ```{r}
 #| context: server
 
-output$spatial_subtype <- renderRglwidget({
-  open3d()
-  bg3d(color = "black")
-  par3d(userMatrix = rotationMatrix(-pi/6, -1, 1, 0), zoom = 0.6)
-  acr.list <- c("MOs","PL","ORBm","ACAd","ILA","DP","ACAv")
-  for(acr in acr.list){
-    mesh <- mesh3d.allen.annot.from.id(get.id.from.acronym(acr))
-    #to.del <- which(mesh$vb[1,] < 0)
-    #to.del <- NA
-    #mesh$it <- mesh$it[,!is.element(mesh$it[1,], to.del) & !is.element(mesh$it[2,], to.del) & !is.element(mesh$it[3,], to.del)]
-    #col <- color.from.acronym(acr)
-    col <- "lightgray"
-    #col <- col_Region[acr]
-    shade3d(mesh, col = col, material = list(lit=FALSE), alpha = 0.1)
-  }
-  
-  df_plot <- [email protected][which(sp.PFC$SubType == input$subtype),]
-  
-  spheres3d(x = df_plot$ML_new, 
-            y = df_plot$DV_new,
-            z = df_plot$AP_new,
-            col = col_cluster[["SubType"]][input$subtype], radius=0.01, alpha=1)
-  rglwidget()
+observeEvent(input$target_3d,{
+  output$spatial_subtype <- renderRglwidget({
+    if (input$target_3d %in% c("ITi-D", "ITi-V", "ITc", "PTi")){
+      df_plot <- [email protected][which(sp.PFC$Proj_module==input$target_3d),]
+    }else{
+      df_plot <- [email protected][which([email protected][,input$target_3d] > 0),]
+    }
+    
+    open3d()
+    bg3d(color = "black")
+    par3d(userMatrix = rotationMatrix(-pi/6, -1, 1, 0), zoom = 0.6)
+    acr.list <- c("MOs","PL","ORBm","ACAd","ILA","DP","ACAv")
+    
+    for(acr in acr.list){
+      mesh <- mesh3d.allen.annot.from.id(get.id.from.acronym(acr))
+      col <- "lightgray"
+      shade3d(mesh, col = col, material = list(lit=FALSE), alpha = 0.1)
+    }
+    
+    spheres3d(x = df_plot$ML_new, 
+              y = df_plot$DV_new,
+              z = df_plot$AP_new,
+              col = col_subtype_target[input$target_3d], radius=0.01, alpha=1)
+    rglwidget()
+  })
 })
-```
-
-
-
-
 
+observeEvent(input$subtype_3d,{
+  output$spatial_subtype <- renderRglwidget({
+    df_plot <- [email protected][which(sp.PFC$SubType == input$subtype_3d),]
+    
+    open3d()
+    bg3d(color = "black")
+    par3d(userMatrix = rotationMatrix(-pi/6, -1, 1, 0), zoom = 0.6)
+    acr.list <- c("MOs","PL","ORBm","ACAd","ILA","DP","ACAv")
+    
+    for(acr in acr.list){
+      mesh <- mesh3d.allen.annot.from.id(get.id.from.acronym(acr))
+      col <- "lightgray"
+      shade3d(mesh, col = col, material = list(lit=FALSE), alpha = 0.1)
+    }
+    
+    spheres3d(x = df_plot$ML_new, 
+              y = df_plot$DV_new,
+              z = df_plot$AP_new,
+              col = col_subtype_target[input$subtype_3d], radius=0.01, alpha=1)
+    rglwidget()
+  })
+})
+```
 
-# raw image
 
-```{=html}
-<iframe src="https://avivator.gehlenborglab.org/?image_url=https://huggingface.co/YAYUhuang/IT_Spatial_dataset/resolve/main/ITslice03.ome.tiff?rel=0&amp;autoplay=1" title="PFC" height="800" width="100%"></iframe>
-```