Adding scripts for reproducing images 2C to 2G

Figures_2CDEF.R

+# script for figures 2C,D,E,F
+
+## loading libraries
+library(Seurat)
+library(ggplot2)
+library(ggplotify)
+library(ggraph)
+library(ggrepel)
+library(ggpubr)
+library(ComplexHeatmap)
+library(gridExtra)
+library(RColorBrewer)
+library(dittoSeq)
+library(openxlsx)
+library(reshape2)
+library(ggalluvial)
+library(dplyr)
+
+# load seurat object
+
+obj <- readRDS("CultureDataset.rds")
+
+# setting color palette:
+
+colpalette <- c("#A6CEE3","#B2DF8A","#FDBF6F","#E78AC3","#FFFF99","#E31A1C","darkgrey")
+
+## Figure 2C
+
+pdf(file = "Fig2C.pdf", width = 4, height = 4)
+dittoSeq::dittoDimPlot(object = obj, reduction.use = "umap.harmony.orig.ident",
+                       var = "Population", opacity = 0.6, do.label = T,labels.size = 5,
+                       labels.highlight = F, labels.repel = T, size = 0.6) + 
+  scale_color_manual(values = colpalette) + 
+  theme(legend.position = "none", plot.title = element_blank(),
+        axis.text = element_text(size = 16, color = "black"))
+dev.off()
+
+## Figure 2D
+
+pdf(file = "Fig2D.pdf", 
+    width = 4, height = 4)
+ggplot(data = g, aes(x = Sample, y = Frequency, alluvium = Population)) +
+  geom_alluvium(aes(fill = Population),
+                alpha = .5, decreasing = FALSE, width = 1/4) +
+  geom_stratum(aes(stratum = Population, fill = Population), alpha = .50, decreasing = FALSE, width = 1/4) + 
+  scale_fill_manual(values = alpha(colour = colpalette, alpha = 0.50)) + 
+  theme_void() + 
+  theme(legend.position = "none",
+        plot.title = element_blank(),
+        axis.title = element_blank(),
+        panel.background = element_rect(fill = "white"),
+        axis.text = element_text(size = 16, color = "black"))
+dev.off()
+
+## Figure 2E
+
+obj_sorted <- subset(obj, cells = WhichCells(object = obj, expression = orig.ident %in% c("S10","S11","S12")))
+
+obj_sorted$Sorting <- obj_sorted$orig.ident
+obj_sorted$Sorting <- gsub(x = obj_sorted$Sorting, pattern = "S10", replacement = "CD38-")
+obj_sorted$Sorting <- gsub(x = obj_sorted$Sorting, pattern = "S11", replacement = "GMP")
+obj_sorted$Sorting <- gsub(x = obj_sorted$Sorting, pattern = "S12", replacement = "MEP")
+obj_sorted$Sorting <- factor(obj_sorted$Sorting, levels = c("CD38-","GMP","MEP"))
+
+cols_sorted <- list("CD38-" = "#008744",
+                    "GMP" = "#0057e7",
+                    "MEP" = "#d62d20"
+)
+
+obj_sorted <- SetIdent(obj_sorted, value = "Sorting")
+obj_sorted$sortcol <- cols_sorted$`CD38-` 
+obj_sorted$sortcol[which(obj_sorted$Sorting == "GMP")] <- cols_sorted$GMP
+obj_sorted$sortcol[which(obj_sorted$Sorting == "MEP")] <- cols_sorted$MEP
+
+p <- dittoDimPlot(object = obj_sorted, var = "Sorting",
+                  color.panel = cols_sorted,
+                  show.others = T,split.nrow = 1,
+                  split.by = "Sorting",
+                  labels.highlight = F,labels.repel = T,
+                  contour.color = "darkgrey",
+                  labels.size = 3.5,do.contour = T,contour.linetype = 2,
+                  reduction.use = "umap.harmony.orig.ident", size = 0.5,
+                  do.label = F) +
+  theme(legend.position = "none",
+        legend.key.size = unit(x = 0.1, units = "in"),
+        strip.background.x = element_rect(fill = "white"),
+        strip.text.x.bottom = element_text(size = 12),
+        plot.title = element_blank(),
+        axis.title = element_blank(),
+        axis.text = element_text(size = 12),
+        panel.border = element_rect())
+
+pdf("Fig2E.pdf", width = 6, height = 2.5)
+p
+dev.off()
+
+## Figure 2F
+
+pdf(file = "Fig2F.pdf", width = 4, height = 4)
+ggplot(data = g, aes(x = Sample, y = Frequency, fill = Population)) +
+  geom_bar(stat = "identity", width = 0.5, color = "black") + 
+  scale_fill_manual(values = alpha(colour = colpalette, alpha = 0.50)) + 
+  theme_void() + 
+  theme(legend.position = "none",
+        plot.title = element_blank(),
+        axis.title = element_blank(),
+        panel.background = element_rect(fill = "white"),
+        axis.text = element_text(size = 16, color = "black"))
+dev.off()
+
+

Figures_2G.R

+# script for figures 2G
+
+## loading libraries
+library(Seurat)
+library(ggplot2)
+library(ggplotify)
+library(ggraph)
+library(ggrepel)
+library(ggpubr)
+library(ComplexHeatmap)
+library(gridExtra)
+library(RColorBrewer)
+library(dittoSeq)
+library(openxlsx)
+library(reshape2)
+library(ggalluvial)
+library(dplyr)
+
+# load seurat object
+
+obj <- readRDS("CultureDataset.rds")
+obj <- subset(obj, cells = WhichCells(object = obj,expression = orig.ident %in% c("C04","C02","C03")))
+obj <- SetIdent(object = obj, value = "Population")
+
+citokine_dotplot_C04_C02_C03 <- DotPlot(object = obj, 
+                                        features = c("KIT","MPL","FLT3","IL6R","IL3RA"),
+                                        dot.min = 0.05,
+                                        scale.by = "size") + 
+  labs(color = "ZscoreExpr", size = "PctExpr")  + 
+  scale_color_gradient2(low = "blue", mid = "lightgrey", high = "red") + 
+  theme(axis.title = element_blank(), 
+        legend.position = "none",           # Places the legend at the bottom
+        legend.justification = "left",       # Justifies the legend to the left
+        legend.box = "vertical"  
+  ) +
+  scale_x_discrete(guide = guide_axis(n.dodge = 2))
+
+pdf(file = "Fig2G.pdf", width = 3, height = 4)
+citokine_dotplot_C04_C02_C03
+dev.off()