Updating script adding code for producing fig2D

Senescence_HSC_Bulk_Focus_fig2C_dataset.R

@@ -11,7 +11,7 @@ library(clusterProfiler)
 library(ComplexHeatmap)
 library(circlize)
 
-outdir <- "HSC_vs_Bulk_Focus_Supplemental_2C/"
+outdir <- "HSC_vs_Bulk_Focus_Supplemental_2CD/"
 dir.create(outdir)
 
 obj_fig2C <- readRDS("Fig2C_Dataset.rds")
@@ -141,3 +141,60 @@ p <- Heatmap(heatmap_mat_t,
 
 draw(p, padding = unit(c(2, 2, 2, 10), "mm")) # c(bottom, left, top, right)
 dev.off()
+
+
+# fig Supplemental 2D
+
+######### only TP53 ########
+
+
+genes <- c( "TP53")
+
+df <- FetchData(
+  object = obj_fig2C_Cs,
+  vars = c(genes, "Timepoint.f", "Group", "GroupTimepoint")
+)
+
+df_long <- df |>
+  tidyr::pivot_longer(
+    cols = all_of(genes),
+    names_to = "Gene",
+    values_to = "expr"
+  )
+
+ggplot(df_long, aes(x = Timepoint.f, y = expr, fill = Group)) +
+  geom_boxplot(position = position_dodge(width = 0.8)) +
+  #facet_wrap(~ Gene, nrow = 1) +
+  theme_bw() +
+  labs(x = "Timepoint", y = "Expression", fill = "Group")
+
+
+# line plot 
+df_summary <- df_long |>
+  group_by(Gene, Timepoint.f, Group) |>
+  summarise(
+    mean_expr = mean(expr),
+    median_expr = median(expr),
+    .groups = "drop"
+  )
+
+mean_plot <- ggplot(df_summary, aes(x = Timepoint.f, y = mean_expr, color = Group, group = Group)) +
+  geom_line() +
+  geom_point() +
+#  facet_wrap(~ Gene, nrow = 1) +
+  theme_bw() +
+  theme(axis.title.x = element_blank())
+
+median_plot <- ggplot(df_summary, aes(x = Timepoint.f, y = median_expr, color = Group, group = Group)) +
+  geom_line() +
+  geom_point() +
+#  facet_wrap(~ Gene, nrow = 1) +
+  theme_bw() +
+  theme(axis.title.x = element_blank())
+
+pdf(file = paste0(outdir, "Fig_S2D_p53_expression_across_culture.pdf"), width = 3, height = 3)
+mean_plot + labs(color = "") + ylab("Average Expression") +
+  ggtitle("TP53 expression") +
+  theme(legend.position = c(0.8,0.2), axis.text = element_text(size = 10),
+        plot.title = element_text(hjust = 0.5))
+dev.off()