Upload New File

WPRE_mapping/MAGIC_imputation_plots.R

+library(Seurat)
+library(Rmagic)
+library(ggplot2)
+library(viridis)
+library(dplyr)
+library(ggpubr)
+library(openxlsx)
+library(gridExtra)
+
+wdir <- "./WPRE_mapping"
+
+# Fig5 A - CART Selection
+df_t <- read.xlsx(xlsxFile = paste("./Clustering_Analysis", "Full_T_Myelo_metadata.xlsx", sep = "/"), sheet = "Tcell", rowNames = T)
+ggplot(df_t, aes(x = UMAPh_1, y = UMAPh_2)) +
+  theme_void(base_size = 12) +
+  theme(legend.position = "none") +
+  geom_point(data = subset(df_t, is.na(CART_MAGIC)), size = pt_size, color = "grey", alpha = .5) +
+  geom_point(data = subset(df_t, CART_MAGIC == "CART_MAGIC"), size = pt_size, color = "darkred", alpha = .5)
+
+# Supplementary Fig11 B - WPRE MAGIC imputation
+df <- read.xlsx(xlsxFile = paste("./Clustering_Analysis", "Full_T_Myelo_metadata.xlsx", sep = "/"), sheet = "Full", rowNames = T)
+
+pt_size <- 0.6
+p1 <- ggplot(df %>% arrange(TGeneCAR_WPRE_count), aes(x = UMAPh_1, y = UMAPh_2, color = TGeneCAR_WPRE_count)) +
+  theme_bw() +
+  theme(legend.position = "top") +
+  xlab("UMAP 1") +
+  ylab("UMAP 2") +
+  scale_color_gradient(low = "grey", high = "darkred", name = "Count") +
+  geom_point(size = pt_size)
+p2 <- ggplot(df %>% arrange(TGeneCAR_WPRE_MAGIC), aes(x = UMAPh_1, y = UMAPh_2, color = TGeneCAR_WPRE_MAGIC)) +
+  theme_bw() +
+  theme(legend.position = "top") +
+  xlab("UMAP 1") +
+  ylab("UMAP 2") +
+  scale_color_gradient(low = "grey", high = "darkred", name = "Imputed") +
+  geom_point(size = pt_size)
+p3 <- ggplot(df, aes(x = TGeneCAR_WPRE_MAGIC)) +
+  theme_bw() +
+  geom_histogram(bins = 150) +
+  geom_vline(xintercept = 0.05, color = "red", linetype = "dashed")
+
+png(filename = paste(wdir, "MAGIC_imputation.png"), width = 1400, height = 400)
+grid.arrange(p1, p2, p3, nrow = 1)
+dev.off()