scripts for reproducing Fig2H and Fig2I

Fig2H.R

+# Source code for producing figure 2H
+
+library(ggplot2)
+library(dplyr)
+library(RColorBrewer)
+library(UCell)
+library(scGate)
+library(viridis)
+library(stringr)   
+library(patchwork)
+library(dittoSeq)
+library(gridExtra)
+library(Seurat)
+library(openxlsx)
+library(ggalluvial)
+library(gridExtra)
+
+obj <- readRDS(file = "Fig2H_dataset.rds")
+
+colpalette <- c("#A6CEE3","#B2DF8A","#FDBF6F","#E78AC3","#FFFF99","#E31A1C","darkgrey","#C4A484")
+
+umap_annot <- dittoSeq::dittoDimPlot(object = obj, reduction.use = "umap.harmony.pt.tp",
+                                     var = "RefinedAnnotation", opacity = 0.8, do.label = T,labels.size = 4,
+                                     labels.highlight = F, labels.repel = T, size = 1,order = "decreasing") + 
+  scale_color_manual(values = colpalette) + 
+  xlab("UMAP_1") +
+  ylab(label = "UMAP_2") +
+  theme(legend.position = "none",
+        legend.title = element_blank(),
+        legend.key.size = unit(0.001, "in"),
+        legend.key.spacing = unit(0,"in"),
+        plot.title = element_blank(),
+        axis.text = element_text(size = 16)
+  )
+
+alluvial_list <- list()
+
+for(pt in c("MPSI001","MPSI004")){
+  
+  meta_tmp <- subset.data.frame(obj@meta.data, subset = Patient == pt)
+  g <- as.data.frame(prop.table(table(meta_tmp[["Timepoint"]], meta_tmp[["RefinedAnnotation"]]), margin = 1)*100)
+  g$Var1 <- factor(g$Var1, levels = c("dp","day4","day7"))
+  bplot_list[[pt]] <- ggplot(data = g, mapping = aes(Var1, Freq, fill = Var2, label = Var2)) + 
+    scale_fill_manual(values = colpalette) + 
+    ggtitle(label = "Classification distribution within Timepoint", subtitle = paste0("Patient ", pt)) + 
+    geom_bar(stat = "identity", width = 0.5, color = "black") + 
+    theme(legend.position = "right",
+          plot.title = element_text(size = 16, hjust = 0.5, face = "plain"),
+          plot.subtitle = element_text(size = 16, hjust = 0.5, face = "plain"),
+          panel.background = element_rect(fill = "white"),
+          axis.line = element_line(colour = "black", size = 0.2),
+          axis.title = element_blank(), 
+          strip.text.x = element_text(size = 12),
+          plot.margin = margin(0.2, 0.2,0.2,0.2, unit = "cm"),
+          axis.text = element_text(size = 16, colour = "black"),
+          legend.title = element_blank(),
+          legend.text = element_text(size = 8),
+          legend.spacing.y = unit(0.1, 'cm'),
+          legend.spacing.x = unit(0.1, 'cm'),
+          legend.key.size = unit(0.5, 'cm'), 
+          legend.key = element_rect(fill = "white"),
+          legend.background = element_blank(),
+          #legend.key.height = unit(0, 'cm'),
+          legend.key.width = unit(0.5, 'cm'),
+          legend.box.margin=margin(-10,0,0,0)
+    ) 
+  alluvial_list[[pt]] <- ggplot(data = g, aes(x = Var1, y = Freq, alluvium = Var2)) +
+    geom_alluvium(aes(fill = Var2),
+                  alpha = .75, decreasing = FALSE, width = 1/3) +
+    geom_stratum(aes(stratum = Var2, fill = Var2), alpha = .50, decreasing = FALSE, width = 1/3) + 
+    scale_fill_manual(values = alpha(colour = colpalette3, alpha = 0.50)) + 
+    theme(legend.position = "right", plot.title = element_blank(),
+          axis.line = element_line(color = "black"),
+          axis.title = element_blank(),
+          panel.background = element_rect(fill = "white"),
+          axis.text = element_text(size = 16))
+}
+
+alluvial_mps1 <- alluvial_list$MPSI001 + NoLegend() + theme(plot.title = element_blank())
+alluvial_mps4 <- alluvial_list$MPSI004 + NoLegend() + theme(plot.title = element_blank())
+
+pdf(file = "Fig2H_panel.pdf", width = 9, height = 3)
+grid.arrange(umap_annot, alluvial_mps1, alluvial_mps4, ncol = 3)
+dev.off()

Fig2I.R

+# Source code for producing figure 2I
+
+library(ggplot2)
+library(dplyr)
+library(RColorBrewer)
+library(UCell)
+library(scGate)
+library(viridis)
+library(stringr)   
+library(patchwork)
+library(dittoSeq)
+library(gridExtra)
+library(Seurat)
+library(openxlsx)
+library(ggalluvial)
+library(gridExtra)
+
+obj <- readRDS(file = "Fig2H_dataset.rds")
+
+umap_wpre <- dittoSeq::dittoDimPlot(object = obj, reduction.use = "umap.harmony.pt.tp",order = "increasing",
+                                    var = "WPRE_condition", opacity = 0.8, do.label = F,labels.size = 4,
+                                    labels.highlight = F, labels.repel = T, size = 1) + 
+  scale_color_manual(values = c("#A0A0A0B3","#FF3333B3")) + 
+  xlab("UMAP_1") +
+  ylab(label = "UMAP_2") +
+  theme(legend.position = "none",
+        legend.title = element_blank(),
+        legend.key.size = unit(0.001, "in"),
+        legend.key.spacing = unit(0,"in"),
+        plot.title = element_blank(),
+        axis.text = element_text(size = 16)
+  )
+
+pdf(file = "Fig2I.pdf", width = 4, height = 4)
+umap_wpre
+dev.off()