Update PFCapp.qmd

PFCapp.qmd

@@ -103,14 +103,15 @@ source("R/Palettes.R")
 source('R/includes.R')
 Adult.Ex <- readRDS('data/Adult.Ex.rds')
 sp.PFC <- readRDS('data/sp.PFC.rds')
+sp.PFC$PTi[is.na(sp.PFC$PTi)] <- 0
+sp.PFC$ITi_D[is.na(sp.PFC$ITi_D)] <- 0
+sp.PFC$ITi_V[is.na(sp.PFC$ITi_V)] <- 0
+sp.PFC$ITc[is.na(sp.PFC$ITc)] <- 0
 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")
-sp.PFC$PTi[is.na(sp.PFC$PTi)] <- 0
-sp.PFC$`ITi-M1`[is.na(sp.PFC$`ITi-M1`)] <- 0
-sp.PFC$`ITi-M2`[is.na(sp.PFC$`ITi-M2`)] <- 0
-sp.PFC$`ITc-M3`[is.na(sp.PFC$`ITc-M3`)] <- 0
+
 
 clean_cells <- colnames(Adult.Ex)[!(
   (Adult.Ex$Ex_subtype %in% c("CT","NP") & Adult.Ex$BC_num>0) | 
@@ -347,7 +348,8 @@ output$sp_gene_plot <- renderPlot({
   df <- df[order(df$Zscore),]
   ggplot(df,aes(x=X,y=Y)) +
     geom_point(aes(colour=Zscore), size=1) +
-    scale_color_gradientn(colours = viridis(n = 256, option = "D", direction = 1)) +
+    scale_color_gradientn(colours = viridis(n = 256, option = "D", direction = 1),
+                          limits = c(0,3)) +
     ggdark::dark_theme_void() +
     labs(title = input$sp_gene) +
     theme(plot.title = element_text(size = 20, hjust = 0.5),
@@ -367,8 +369,7 @@ output$sp_target_plot <- renderPlot({
   df <- df[order(df$Zscore),]
   ggplot(df, aes(x=X,y=Y)) +
     geom_point(aes(colour=Zscore), size=1) +
-    scale_color_gradientn(colours = viridis(n = 256, option = "E", direction = 1),
-                          limits = c(0,3)) +
+    scale_color_gradientn(colours = viridis(n = 256, option = "E", direction = 1)) +
     ggdark::dark_theme_void() +
     labs(title = input$sp_target) +
     theme(plot.title = element_text(size = 20, hjust = 0.5),