Merge pull request #387 from LCSB-BioCore/mo-makie

Use Makie instead of Plots

docs/Project.toml

 [deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 OSQP = "ab2f91bb-94b4-55e3-9ba0-7f65df51de79"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
-Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 
 [compat]
 Documenter = "0.26"

docs/src/notebooks/6_screening.jl

@@ -52,8 +52,18 @@ productions = screen_variants(
 # This can be nicely plotted to give a more comprehensive overview of which
 # reactions are critical or not:
 
-using Plots
-bar(reactions(model), productions, orientation = :hor, dpi = 600)
+using CairoMakie
+
+disp_rxns = rand(1:95, 20) # only display 20 random fluxes to save space
+barplot(
+    productions[disp_rxns],
+    direction = :x,
+    axis = (
+        yticks = (1:20, reactions(model)[disp_rxns]),
+        xlabel = "Flux [mmol/gDW/h]",
+        ylabel = "Reaction ID",
+    ),
+)
 
 # ## Knocking out reaction combinations
 #
@@ -77,4 +87,15 @@ productions = screen_variants(
     model -> get_biomass(flux_balance_analysis_dict(model, Tulip.Optimizer)),
 )
 
-heatmap(productions, dpi = 600)
+f = Figure()
+ax = Axis(
+    f[1, 1],
+    ylabel = "Reaction KO",
+    xlabel = "Reaction KO",
+    yticks = (1:20, reactions(model)[disp_rxns]),
+    xticks = (1:20, reactions(model)[disp_rxns]),
+    xticklabelrotation = -pi / 4,
+)
+hm = heatmap!(ax, productions[disp_rxns, disp_rxns])
+Colorbar(f[1, 2], hm, label = "Flux [mmol/gDW/h]")
+f