Upload Analysis Script

Clustering_Analysis/Paper_figures.R

+library(Seurat)
+library(ggplot2)
+library(dplyr)
+library(openxlsx)
+
+# Set Folders
+wdir <- "./Clustering_Analysis"
+
+# Figure 5A - Center
+df <- read.xlsx(xlsxFile = paste(wdir, "Full_T_Myelo_metadata.xlsx", sep = "/"), sheet = "Full")
+df$AnnotationRaw <- as.factor(df$AnnotationRaw)
+
+p <- ggplot(data = df, mapping = aes(x = UMAPh_1, y = UMAPh_2, color = AnnotationRaw)) +
+  theme_void(base_size = 12) +
+  theme(legend.position = "none") +
+  geom_point(size = .3)
+Seurat::LabelClusters(plot = p, id = "AnnotationRaw", color = "black", size = 5)
+
+# Figure 5A - T cells
+df_t <- read.xlsx(xlsxFile = paste(wdir, "Full_T_Myelo_metadata.xlsx", sep = "/"), sheet = "Tcell")
+df_t$Annotation <- as.factor(df_t$Annotation)
+
+p_t <- ggplot(data = df_t, mapping = aes(x = UMAPh_1, y = UMAPh_2, color = Annotation)) +
+  theme_void(base_size = 12) +
+  theme(legend.position = "none") +
+  geom_point(size = .6)
+Seurat::LabelClusters(plot = p_t, id = "Annotation", color = "black", size = 5)
+
+ggplot(data = df_t, mapping = 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 = .6, color = "grey80") +
+  geom_point(data = subset(df_t, CART_MAGIC == "CART_MAGIC"), size = .6, color = "darkred")
+
+# Figure 5A - Myeloid cells
+df_m <- read.xlsx(xlsxFile = paste(wdir, "Full_T_Myelo_metadata.xlsx", sep = "/"), sheet = "Myeloid")
+df_m$Annotation <- as.factor(df_m$Annotation)
+p_m <- ggplot(data = df_m, mapping = aes(x = UMAPh_1, y = UMAPh_2, color = Annotation)) +
+  theme_void(base_size = 12) +
+  theme(legend.position = "none") +
+  geom_point(size = .6)
+Seurat::LabelClusters(plot = p_m, id = "Annotation", color = "black", size = 5)
+