Update PFCdevApp.qmd

PFCdevApp.qmd

@@ -55,13 +55,7 @@ Spatial data
 </p>
 
 <p style="font-size: 20px; text-align: justify;">
-We collected the whole brain stereo-seq datasets of P1 and Adult mice from [(Han et al., Neuron, 2025)](https://doi.org/10.1016/j.neuron.2025.02.015
-        
-        
-        
-        
-        
-        , extracted and analyzed the PFC brain region. Users can browse the following content through the spatial page:
+We collected the whole brain stereo-seq datasets of P1 and Adult mice from [(Han et al., Neuron, 2025)](https://doi.org/10.1016/j.neuron.2025.02.015, extracted and analyzed the PFC brain region. Users can browse the following content through the spatial page:
 </p>
 
 - Spatial Clustering: Select different cell subtypes to view their spatial distribution
@@ -98,6 +92,10 @@ seu.downsample$orig.ident[seu.downsample$orig.ident == "P0"] <- "P1"
 seu.downsample$orig.ident <- factor(seu.downsample$orig.ident,
                                     levels = c("P1","P4","P10","Adult"))
 seu.downsample$SubType <- seu.downsample$SubType_v4
+seu.downsample$SubType <- factor(seu.downsample$SubType, 
+                                 levels = names(col_cluster[["SubType"]]))
+seu.downsample$MainType <- factor(seu.downsample$MainType,
+                                  levels = names(col_cluster[["MainType"]]))
 
 # spatial
 column <- c("x_rotated","y_rotated","Im.L2.3.IT","Im.L4.5.IT","Im.L5.IT","Im.L6.IT","L2.3.IT","L4.5.IT","L5.IT","L6.IT","L5.PT","L5.NP","L6.CT","Lamp5","Pvalb","Sst","Vip","NPC","Astro","Endo","Microglia","Oligo","OPC")
@@ -159,35 +157,36 @@ plotOutput('cluster_plot')
 
 #### Column
 
-
 ```{r}
-plotOutput('vln_plot')
+plotOutput('gene_plot')
 ```
 
+
 ### Row
 
 #### Column
 
 ```{r}
-plotOutput('gene_plot')
+plotOutput('vln_plot')
 ```
 
 
 ```{r}
 #| context: server
 
-output$cluster_plot <- renderPlot({
+seu <- reactive({
   if (input$dataset=="Neurons"){
-    seu <- subset(seu.downsample, cells = colnames(seu.downsample)[seu.downsample$MainType %in% c("Excitatory", "Inhibitory")])
+    subset(seu.downsample, 
+           cells = colnames(seu.downsample)[seu.downsample$MainType %in%
+                                              c("Excitatory", "Inhibitory")])
   }else{
-    seu <- seu.downsample
+    seu.downsample
   }
-  seu@meta.data[,input$celltype] <- factor(
-    seu@meta.data[,input$celltype],
-    levels = names(col_cluster[[input$celltype]])
-  )
+})
+
+output$cluster_plot <- renderPlot({
     DimPlot(
-      seu,
+      seu(),
       reduction = 'umap',
       group.by = input$celltype,
       split.by = "orig.ident",
@@ -204,30 +203,10 @@ output$cluster_plot <- renderPlot({
       guides(color = guide_legend(ncol = 1, override.aes = list(size = 3)))
 })
 
-output$vln_plot <- renderPlot({
-  if (input$dataset=="Neurons"){
-    seu3 <- subset(seu.downsample, cells = colnames(seu.downsample)[seu.downsample$MainType %in% c("Excitatory", "Inhibitory")])
-  }else{
-    seu3 <- seu.downsample
-  }
-  seu3@meta.data[,input$celltype] <- factor(
-    seu3@meta.data[,input$celltype],
-    levels = names(col_cluster[[input$celltype]])
-  )
-  VlnPlot(seu.downsample, features = input$gene, group.by = input$celltype,
-          col = col_cluster[[input$celltype]]) +
-    NoLegend() +
-    labs(x="")
-})
 
 output$gene_plot <- renderPlot({
-  if (input$dataset=="Neurons"){
-    seu <- subset(seu.downsample, cells = colnames(seu.downsample)[seu.downsample$MainType %in% c("Excitatory", "Inhibitory")])
-  }else{
-    seu <- seu.downsample
-  }
   FeaturePlot(
-    seu,
+    seu(),
     features = input$gene,
     reduction = 'umap',
     split.by = "orig.ident",
@@ -242,10 +221,15 @@ output$gene_plot <- renderPlot({
     coord_fixed() &
     scale_color_gradientn(colours = c("lightblue3", "lightblue", "white", "red", "red4"), limits=c(0,2), breaks=c(0,2), na.value = "red4")
 })
-```
-
 
 
+output$vln_plot <- renderPlot({
+  VlnPlot(seu(), features = input$gene, group.by = input$celltype,
+          col = col_cluster[[input$celltype]]) +
+    NoLegend() +
+    labs(x="")
+})
+```