# Figure 1C and 1D
p1 = DimPlot2(Bf.combined.youngBrain, reduction = 'tsne', group.by = 'integrated_snn_res.1', label = T, pt.size = 0.01)
p2 = DimPlot2(Bf.combined.youngSC, reduction = 'tsne', group.by = 'integrated_snn_res.1', label = T, pt.size = 0.01)
plot_grid(p1, p2, ncol = 2, rel_widths = c(1,1))

# Figure 1E and 1F
p1 = DimPlot2(Bf.combined.young, group.by = "tissue", reduction = "tsne", cols = c("#f8766d", "#00bfc4"))
p2 = FeaturePlot_scCustom(Bf.combined.young, features = "BrainIndex", reduction = "tsne", na_cutoff= 0, order = F, label = T, repel = T, pt.size = 0.01, col= rev(hcl.colors(18, "RdYlBu")))
plot_grid(p1, p2, ncol = 2, rel_widths = c(1,1))

# Figure 1G and 1H
p1 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "BrainIndex", reduction = "tsne", na_cutoff= 75, order = F, label = T, repel = T, pt.size = 0.01, col = rev(hcl.colors(18, "Reds2")))
p2 = FeaturePlot_scCustom(Bf.combined.youngSC, features = "SCIndex", reduction = "tsne", na_cutoff= 75, order = F, label = T, repel = T, pt.size = 0.01, col = rev(hcl.colors(18, "Greens2")))
plot_grid(p1, p2, ncol = 2, rel_widths = c(1,1))

# Figure 1I and S4
p1 = DimPlot2(Bf.combined.youngBrain, order = FALSE, reduction = "tsne", label = T, repel = F, pt.size = 0.01, group.by = "integrated_snn_res.1", theme = NoLegend())  + NoLegend()
p2 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118419299", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # Snap 25
p3 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118403268", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # Map2
p4 = DimPlot(Bf.combined.youngBrain, order = FALSE, reduction = "tsne", label = F, repel = F, pt.size = 0.01, group.by = "Level1", cols = c("#dab1da", "lightgreen"))+ NoLegend()
p5 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118422398", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # Quaking
p6 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118406629", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # EAAT
plot_grid(p1, p2, p3, p4, p5, p6, ncol = 3, align = 'none', rel_widths = c(1,1,1))

# Figure 1J and S5
p1 = DimPlot2(Bf.combined.youngBrain, order = FALSE, reduction = "tsne", label = T, repel = F, pt.size = 0.01, group.by = "integrated_snn_res.1", theme = NoLegend())  + NoLegend() 
p2 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118413152", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # VGluT1
p3 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118412582", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # VAChT
p4 = DimPlot(Bf.combined.youngBrain, order = FALSE, reduction = "tsne", label = F, repel = F, pt.size = 0.01, group.by = "Level2", cols = c("firebrick3", "navy", "#ffe200", "lightgreen")) + NoLegend()
p5 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118403707", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # Gad1
p6 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118410293", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # VIAAT
p7 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118413796", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # VMATa
p8 = FeaturePlot_scCustom(Bf.combined.youngBrain, features = "LOC118412921", reduction = "tsne", label = F, repel = F, pt.size = 0.01) + NoLegend() # VMATb
plot_grid(p1, p2, p3, p4, p5, p6, NA , p7, p8, ncol = 3, align = 'none', rel_widths = c(1,1,1))
