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Figure2.jl
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Figure2.jl
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import CellScopes as cs
## whole kidney
alpha_trans=1
anno2 = Dict("Podo" => ("magenta1",alpha_trans), "HealthyPT"=>("green3",alpha_trans), "InjPT"=>("#f92874",alpha_trans),"TAL"=>("lightslateblue",alpha_trans),
"DCT"=>("blue",alpha_trans),"CD-PC"=>("turquoise1",alpha_trans),"CD-IC"=>("#924cfa",alpha_trans),"vEC"=>("firebrick",alpha_trans),
"gEC"=>("dodgerblue",alpha_trans),"Fib"=>("#edff4d",alpha_trans),"JGA"=>("sienna2",alpha_trans),"Immune"=>("darkgreen",alpha_trans), "Uro"=>("black",alpha_trans));
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2,x_lims=(0,35000),
y_lims=(0,40000), width=5000,height=6000,
stroke_color="gray80")
## artery
anno2 = Dict("Podo" => ("white",alpha_trans),
"HealthyPT"=>("white",alpha_trans),
"InjPT"=>("white",alpha_trans),
"TAL"=>("white",alpha_trans),
"DCT"=>("white",alpha_trans),
"CD-PC"=>("white",alpha_trans),
"CD-IC"=>("white",alpha_trans),
"vEC"=>("firebrick",alpha_trans),
"gEC"=>("white",alpha_trans),
"Fib"=>("#edff4d",alpha_trans),
"JGA"=>("white",alpha_trans),
"Immune"=>("white",alpha_trans),
"Uro"=>("white",alpha_trans));
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2, x_lims=(21900,24500), y_lims=(11500,19500),
width=300,height=900,stroke_color="gray80")
## podocyte
anno2 = Dict("Podo" => ("magenta1",alpha_trans),
"HealthyPT"=>("white",alpha_trans),
"InjPT"=>("white",alpha_trans),
"TAL"=>("white",alpha_trans),
"DCT"=>("white",alpha_trans),
"CD-PC"=>("white",alpha_trans),
"CD-IC"=>("white",alpha_trans),
"vEC"=>("white",alpha_trans),
"gEC"=>("dodgerblue",alpha_trans),
"Fib"=>("white",alpha_trans),
"JGA"=>("sienna2",alpha_trans),
"Immune"=>("white",alpha_trans),
"Uro"=>("white",alpha_trans))
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2, x_lims=(17800,20000), y_lims=(8700,9600),
width = 600,height = 250,stroke_color="gray80")
## cortex
anno2 = Dict("Podo" => ("magenta1",alpha_trans),
"HealthyPT"=>("green3",alpha_trans),
"InjPT"=>("#f92874",alpha_trans),
"TAL"=>("lightslateblue",alpha_trans),
"DCT"=>("blue",alpha_trans),
"CD-PC"=>("turquoise1",alpha_trans),
"CD-IC"=>("#924cfa",alpha_trans),
"vEC"=>("firebrick",alpha_trans),
"gEC"=>("dodgerblue",alpha_trans),
"Fib"=>("#edff4d",0.5),
"JGA"=>("sienna2",alpha_trans),
"Immune"=>("darkgreen",alpha_trans),
"Uro"=>("black",alpha_trans))
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2, x_lims=(23000,24800), y_lims=(7400,9000),
width=450,height=400,stroke_color="gray80")
## outer medulla
anno2 = Dict("Podo" => ("magenta1",alpha_trans),
"HealthyPT"=>("green3",alpha_trans),
"InjPT"=>("#f92874",alpha_trans),
"TAL"=>("lightslateblue",alpha_trans),
"DCT"=>("blue",alpha_trans),
"CD-PC"=>("turquoise1",alpha_trans),
"CD-IC"=>("#924cfa",alpha_trans),
"vEC"=>("firebrick",alpha_trans),
"gEC"=>("dodgerblue",alpha_trans),
"Fib"=>("#edff4d",0.5),
"JGA"=>("sienna2",alpha_trans),
"Immune"=>("darkgreen",alpha_trans),
"Uro"=>("black",alpha_trans))
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2, x_lims=(18300,19800), y_lims=(10700,14000),
width=300,height=600,stroke_color="gray80")
## inner medulla
anno2 = Dict("Podo" => ("magenta1",alpha_trans),
"HealthyPT"=>("green3",alpha_trans),
"InjPT"=>("#f92874",alpha_trans),
"TAL"=>("lightslateblue",alpha_trans),
"DCT"=>("blue",alpha_trans),
"CD-PC"=>("turquoise1",alpha_trans),
"CD-IC"=>("#924cfa",alpha_trans),
"vEC"=>("firebrick",alpha_trans),
"gEC"=>("dodgerblue",alpha_trans),
"Fib"=>("#edff4d",0.5),
"JGA"=>("sienna2",alpha_trans),
"Immune"=>("darkgreen",alpha_trans),
"Uro"=>("black",alpha_trans))
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2, x_lims=(15000,17000), y_lims=(16000,20000),
width=300,height=600,stroke_color="gray40")
## papilla
anno2 = Dict("Podo" => ("magenta1",alpha_trans),
"HealthyPT"=>("green3",alpha_trans),
"InjPT"=>("#f92874",alpha_trans),
"TAL"=>("lightslateblue",alpha_trans),
"DCT"=>("blue",alpha_trans),
"CD-PC"=>("turquoise1",alpha_trans),
"CD-IC"=>("#924cfa",alpha_trans),
"vEC"=>("firebrick",alpha_trans),
"gEC"=>("dodgerblue",alpha_trans),
"Fib"=>("#edff4d",0.5),
"JGA"=>("sienna2",alpha_trans),
"Immune"=>("darkgreen",alpha_trans),
"Uro"=>("black",alpha_trans));
cs.plot_cell_polygons(sham, "celltype";
cell_colors=anno2, x_lims=(14300,16300), y_lims=(22900,24900),
width=400,height=400,stroke_color="gray40")