Update PFCapp.qmd

PFCapp.qmd

@@ -9,9 +9,6 @@ format:
       - icon: github
         href: https://github.com/ZhengTiger/SPIDER-Seq
 ---
-
-
-
 # Home
 
 <p style="font-size: 50px; font-weight: bold; text-align: center;">Modular organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIEDER-Seq</p>
@@ -106,12 +103,20 @@ source("R/Palettes.R")
 source('R/includes.R')
 Adult.Ex <- readRDS('data/Adult.Ex.rds')
 sp.PFC <- readRDS('data/sp.PFC.rds')
+sp.PFC$Proj_module[which(sp.PFC$Proj_module=="ITi-D")] <- "ITi-M1"
+sp.PFC$Proj_module[which(sp.PFC$Proj_module=="ITi-V")] <- "ITi-M2"
+sp.PFC$Proj_module[which(sp.PFC$Proj_module=="ITc")] <- "ITc-M3"
+colnames([email protected])[match(c("ITi_D","ITi_V","ITc"),colnames([email protected]))] <- c("ITi-M1","ITi-M2","ITc-M3")
 
 clean_cells <- colnames(Adult.Ex)[!(
   (Adult.Ex$Ex_subtype %in% c("CT","NP") & Adult.Ex$BC_num>0) | 
   (Adult.Ex$sample %in% c("Adult2","Adult3") & Adult.Ex$Ex_subtype=="PT" & Adult.Ex$BC_num>0)
   )]
 Adult.Ex.clean <- subset(Adult.Ex, cells = clean_cells)
+Adult.Ex.clean$Proj_module[which(Adult.Ex.clean$Proj_module=="ITi-D")] <- "ITi-M1"
+Adult.Ex.clean$Proj_module[which(Adult.Ex.clean$Proj_module=="ITi-V")] <- "ITi-M2"
+Adult.Ex.clean$Proj_module[which(Adult.Ex.clean$Proj_module=="ITc")] <- "ITc-M3"
+colnames([email protected])[match(c("ITi_D_score", "ITi_V_score", "ITc_score", "PTi_score"),colnames([email protected]))] <- c("ITi-M1", "ITi-M2","ITc-M3","PTi")
 
 options(rgl.useNULL = TRUE)
 ```
@@ -135,7 +140,7 @@ selectInput('gene', 'Select Gene', rownames(Adult.Ex),
 
 ```{r}
 Barcode <- c(
-  "ITi-D", "ITi-V", "ITc", "PTi",
+  "ITi-M1", "ITi-M2", "ITc-M3", "PTi",
   'VIS-I','SSp-I','CP-I','AUD-I','RSP-I',
   'BLA-I','ACB-I','ENTl-I','AId-I','ECT-I',
   'ACB-C','PL-C','ECT-C','ENTl-C',
@@ -199,7 +204,7 @@ output$gene_plot <- renderPlot({
 
 output$target_plot <- renderPlot({
   Barcode <- c(
-    "ITi-D", "ITi-V", "ITc", "PTi",
+    "ITi-M1", "ITi-M2","ITc-M3","PTi",
     'VIS-I','SSp-I','CP-I','AUD-I','RSP-I',
     'BLA-I','ACB-I','ENTl-I','AId-I','ECT-I',
     'ACB-C','PL-C','ECT-C','ENTl-C',
@@ -207,7 +212,6 @@ output$target_plot <- renderPlot({
     'MD-I','RE-I','DR-I','VTA-I','LHA-I','SC-I'
     )
   seu <- Adult.Ex.clean
-  colnames([email protected])[match(c("ITi_D_score", "ITi_V_score", "ITc_score", "PTi_score"),colnames([email protected]))] <- c("ITi-D", "ITi-V","ITc","PTi")
   [email protected][,Barcode][is.na([email protected][,Barcode])] <- 0
   FeaturePlot(
     seu, features = input$target, order = T) +
@@ -216,7 +220,7 @@ output$target_plot <- renderPlot({
 
 output$target_bar_plot <- renderPlot({
   seu <- Adult.Ex.clean
-  if (input$target %in% c("ITi-D", "ITi-V","ITc","PTi")){
+  if (input$target %in% c("ITi-M1", "ITi-M2","ITc-M3","PTi")){
     df <- as.data.frame(table([email protected][,input$cluster][which(seu$Proj_module==input$target)]))
   }else{
     df <- as.data.frame(table([email protected][,input$cluster][which([email protected][,input$target]>0)]))
@@ -258,7 +262,7 @@ selectInput('sp_gene', 'Select Gene', rownames(sp.PFC),
 
 ```{r}
 sp_Barcode <- c(
-  "ITi-D", "ITi-V", "ITc", "PTi",
+  "ITi-M1", "ITi-M2","ITc-M3","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',
@@ -317,7 +321,7 @@ output$sp_cluster_plot <- renderPlot({
   ggplot(df, aes(x=x, y=y, color=type)) +
     geom_point(size=1) +
     scale_color_manual(values = col_cluster[[input$sp_cluster]]) +
-    labs(title = paste(input$slice,'cell types in spatial')) +
+    labs(title = paste(input$slice,'Cell types in spatial')) +
     guides(color=guide_legend(nrow = 2, byrow = TRUE, reverse = T,
                               override.aes = list(size=2))) +
     coord_fixed() +
@@ -350,10 +354,10 @@ output$sp_gene_plot <- renderPlot({
 output$sp_target_plot <- renderPlot({
   seu <- sp.PFC
   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
-  colnames([email protected])[match(c("ITi_D","ITi_V"),colnames([email protected]))] <- c("ITi-D","ITi-V")
+  seu$`ITi-M1`[is.na(seu$`ITi-M1`)] <- 0
+  seu$`ITi-M2`[is.na(seu$`ITi-M2`)] <- 0
+  seu$`ITc-M3`[is.na(seu$`ITc-M3`)] <- 0
+
   df <- data.frame(
     X = seu$ML_new,
     Y = seu$DV_new,
@@ -379,7 +383,7 @@ output$sp_target_line_plot <- renderPlot({
   slice <- unique(seu$slice)
   df <- data.frame('slice'=slice)
   for (i in 1:length(slice)){
-    if (input$sp_target %in% c("ITi-D","ITi-V","ITc","PTi")){
+    if (input$sp_target %in% c("ITi-M1","ITi-M2","ITc-M3","PTi")){
       df$cellnum[i] <- length(which(seu$slice==slice[i] & seu$Proj_module==input$sp_target))/length(which(seu$slice==slice[i] & seu$BC_num>0))
     }else{
       df$cellnum[i] <- length(which(seu$slice==slice[i] & [email protected][,input$sp_target]>0))/length(which(seu$slice==slice[i] & seu$BC_num>0))
@@ -396,13 +400,12 @@ output$sp_target_line_plot <- renderPlot({
     labs(x='A → P',y='Cell proportion')
   
   # DV
-  sp_Barcode <- c("ITi-D", "ITi-V", "ITc", "PTi",
+  sp_Barcode <- c("ITi-M1","ITi-M2","ITc-M3", "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')
   seu <- subset(sp.PFC, cells=colnames(sp.PFC)[which(sp.PFC$ABA_hemisphere=="Left")])
-  colnames([email protected])[match(c("ITi_D","ITi_V"),colnames([email protected]))] <- c("ITi-D","ITi-V")
   bc_slice <- [email protected][,c(sp_Barcode, 'Y','BC_num')]
   bc_slice <- 
     bc_slice |>
@@ -438,7 +441,7 @@ output$sp_target_line_plot <- renderPlot({
 ## {.sidebar}
 
 ```{r}
-sp_Barcode <- c("ITi-D", "ITi-V", "ITc", "PTi",
+sp_Barcode <- c("ITi-M1","ITi-M2","ITc-M3", "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',
@@ -462,7 +465,7 @@ rglwidgetOutput('spatial_subtype', width = "100%")
 observeEvent(input$target_3d,{
   waiter::Waiter$new(id = "spatial_subtype", color="black")$show()
   output$spatial_subtype <- renderRglwidget({
-    if (input$target_3d %in% c("ITi-D", "ITi-V", "ITc", "PTi")){
+    if (input$target_3d %in% c("ITi-M1","ITi-M2","ITc-M3", "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),]