Update HBplot.R

Single_cell_RNAseq_10x/HBplot.R

@@ -1,35 +1,50 @@
-feats <- read.table("data/list_TR1.txt")$V1
-
+feats <- features
+fc <- 0.3
 #Modifications to SC table
-sc <- sc %>% mutate(expression = ifelse(abs(avg_log2FC) < 1, 
-                                            "NS", "SIG")) %>% 
-mutate(expression = ifelse(gene %in% feats,
-                                            "107", expression))
+v0 <- v0 %>% mutate(expression = ifelse(abs(avg_log2FC) < fc, 
+                                            "No Significant",
+                                        "Significant"
+                                        ),
+                    expression = ifelse(gene %in% feats,
+                                        "Suppl table 1 gene list",
+                                         expression),
+                    expression = factor(expression,
+                                        levels=c("No Significant", "Significant",
+                                                 "Suppl table 1 gene list"))
+
+            )
 
 set.seed(1)
-p <- sc %>% ggplot(aes(avg_log2FC, cluster)) +
-geom_jitter(data = sc,
+p <- v0 %>% ggplot(aes(avg_log2FC, celltype)) +
+geom_jitter(data = v0,
     size = 1.5, aes(color = expression),
     position = position_jitter(seed = 1))+
-geom_label_repel(data = sc,
+geom_label_repel(data = v0,
      aes(label = ifelse((gene %in% feats) | 
-     (abs(avg_log2FC) > 1.5 & !(gene %in% features)),
+     (abs(avg_log2FC) > fc & !(gene %in% feats)),
                                           gene, NA),
                            color = expression),
                        size = 2.5,
                        force = 1,
                        vjust = -0.1,
                        max.overlaps = 7,
-                      position = position_jitter(seed = 1))+
+                      position = position_jitter(seed = 1),show.legend = F)+
       scale_x_continuous(trans = pseudolog10_trans,
                          limits = symmetric_limits) +
-      scale_color_manual(labels = c("107 Gene List", "Non Significant",
-                                    "Significant"),
-                         values = c("red", "grey", "darkgreen")) +
-      ylab("Cluster") +
-      xlab("Avglog2FC DE genes") +
-      theme_bw()+
-      theme(axis.ticks.y = element_blank(), axis.text.y = element_blank(), 
-            axis.title.y = element_blank()
-      )+
-      labs(title = paste0("DE analysis: ", check[i], " vs ", check[j]))
+      scale_color_manual(values = c("grey", "darkgreen", "red")) +
+      xlab("log2 Fold Change") +
+  geom_vline(xintercept = c(-fc, fc), linetype = 2, size = 0.3, col = "grey20")+
+      ggprism::theme_prism()+
+  ggtitle("5 weeks vs 10 weeks")+
+  theme(
+        axis.title.x = element_text(size = 20),
+        axis.text.x = element_text(size = 16),
+        axis.text.y = element_text(size = 18, face="bold"),
+        axis.title.y = element_blank(),
+        legend.text = element_text(size=16),
+        legend.position = "bottom",
+        legend.justification = "center",
+        legend.title = element_blank(),
+        plot.title = element_text(size=24, face="bold", hjust=0.5)
+                  )+
+  guides(color = guide_legend(override.aes = list(size=3)))