# Figure 2C
DimPlot(xenium.2022.obj.neurons.log.rotated, label = T, repel = T, reduction = "tsne", group.by = "Xenium_snn_res.1.5", pt.size = 0.01, cols = c(
"#ffabc3", #0
"#ff567a", #1
"#ffb0ab", #2
"#ff6020", #3
"#ffb584", #4
"#d38600", #5
"#ffbc3a", #6
"#c79000", #7
"#f9c400", #8
"#bf9800", #9
"#eecd00", #10
"#b3a200", #11
"#d9da00", #12
"#98af00", #13
"#4bf600", #14
"#00c259", #15
"#00f7a8", #16
"#00bf99", #17
"#00f3d8", #18
"#00bcb5", #19
"#00edf9", #20
"#00b4d0", #21
"#89dcff", #22
"#00a8f6", #23
"#a9ceff", #24
"#6796ff", #25
"#b9c3ff", #26
"#8c86ff", #27
"#c7b9ff", #28
"#a877ff", #29
"#d8b1ff", #30
"#ca62ff", #31
"#f3a5ff", #32
"#fd28f1", #33
"#ffa5e0", #34
"#ff48ae" #35

  )) + theme(aspect.ratio = 1)


# Figure 2E
DimPlot(xenium.2022.obj.neurons.log.rotated, label = F, repel = T, reduction = "tsne", group.by = "Level1", pt.size = 0.01, cols = c( 
             "#CF8EB1", # "anterior forebrain"
             "#E41A1C", # "infundibular organ (IO)"
             "#FF7F00", # "dorsal Layer",
             "#C1862A", # "cells of Joseph",
             "#F1E330", # "dorsal ventricular cavity",
             "#FECB20", # "translumenal cells I (anterior)",
             "#CF8E4D", # "boundary cells I",
             "#A65628", # "boundary cells II",
             "#984EA3", # "translumenal cells II (posterior-upper)",
             "#728A7A", # "translumenal cells III (posterior-lower)",
             "#549F6C", # "central canal",
             "#377EB8", # "nucleus of Rohde (nRo)",
             "#BFD1C4", # "migrated cells",
             "#9C3EFF"# "others"
  )) + theme(aspect.ratio = 1)