diff --git a/article/figures/fig2.pdf b/article/figures/fig2.pdf new file mode 100644 index 0000000..372a9cc Binary files /dev/null and b/article/figures/fig2.pdf differ diff --git a/article/figures/fig2d.pdf b/article/figures/fig2d.pdf new file mode 100644 index 0000000..7fcd354 Binary files /dev/null and b/article/figures/fig2d.pdf differ diff --git a/article/figures/fig3.pdf b/article/figures/fig3.pdf new file mode 100644 index 0000000..fe4d116 Binary files /dev/null and b/article/figures/fig3.pdf differ diff --git a/article/figures/fig4.pdf b/article/figures/fig4.pdf new file mode 100644 index 0000000..c42b7d9 Binary files /dev/null and b/article/figures/fig4.pdf differ diff --git a/article/figures/fig5.pdf b/article/figures/fig5.pdf new file mode 100644 index 0000000..2b19719 Binary files /dev/null and b/article/figures/fig5.pdf differ diff --git a/article/figures/figS1.pdf b/article/figures/figS1.pdf new file mode 100644 index 0000000..2d1b62c Binary files /dev/null and b/article/figures/figS1.pdf differ diff --git a/code/figure2.jl b/code/figure2.jl index d2371f5..45fb3b7 100644 --- a/code/figure2.jl +++ b/code/figure2.jl @@ -24,11 +24,11 @@ fig2c = plot(sol, vars = (0, 3), xlim = (5000, 6500), ylim = (7, 10.5), ) #2c fig2 = plot(fig2a, fig2b, fig2c, layout = (3,1), - size = (500, 900), titlefontsize = 15, - tickfontsize = 15, guidefontsize = 15, + size = (500, 900), titlefontsize = 11, + tickfontsize = 8, guidefontsize = 10, left_margin = 8Plots.mm, right_margin = 5Plots.mm, bottom_margin = 2Plots.mm, framestyle = :box ) ## Export figures -savefig(fig2, joinpath("..", "article", "figures", "fig2")) +savefig(fig2, joinpath("..", "article", "figures", "fig2.pdf")) diff --git a/code/figure2D.jl b/code/figure2D.jl index 937db32..b1d96ee 100644 --- a/code/figure2D.jl +++ b/code/figure2D.jl @@ -17,13 +17,12 @@ sol_y_b3 = sol_b3[2, :] # timeseries for y sol_z_b3 = sol_b3[3, :] # timeseries for z # Teacup Figures 2D and 5E (Three-dimensional phase plot) -gr() fig2d = plot(sol_x_b3, sol_y_b3, sol_z_b3, # sol_b3, vars = (1,2,3), - linewidth = 0.01, linestyle = :dot, + linestyle = :dot, xlabel = "x", xflip = false, xlim = (0.0, 1.0), xticks = 0.0:0.5:1.0, ylabel = "y", yflip = true, ylim = (0.0, 0.5), yticks = 0.0:0.25:0.5, zlabel = "z", zflip = false, zlim = (7.5, 10.5), zticks = 7.5:1.5:10.5, - tick_direction = :out, guidefontsize = 12, tickfontsize = 12, + tick_direction = :out, guidefontsize = 10, tickfontsize = 8, legend = :none, size = (600, 600), c = :black, right_margin = 5Plots.mm, left_margin = 2Plots.mm, ) @@ -32,11 +31,11 @@ fig2d = plot(sol_x_b3, sol_y_b3, sol_z_b3, # sol_b3, vars = (1,2,3), sol_y_b3_flip = copy(sol_y_b3) sol_y_b3_flip = 0.5 .- sol_y_b3_flip fig2d_flip = plot(sol_x_b3, sol_y_b3_flip, sol_z_b3, #sol_b3,vars=(1,2,3), - linewidth = 0.01, linestyle = :dot, + linestyle = :dot, xlabel = "x", xflip = false, xlim = (0.0, 1.0), xticks = 0.0:0.5:1.0, xrotation = 30.0, ylabel = "y", yflip = false, ylim = (0.0, 0.5), yticks = (0.0:0.25:0.5, string.(0.5:-0.25:0.0)), yrotation=-10.0, zlabel = "z", zflip = false, zlim = (7.5, 10.5), zticks = 7.5:1.5:10.5, zrotation=0.0, - tick_direction=:out, guidefontsize = 12, tickfontsize = 12, + tick_direction=:out, guidefontsize = 10, tickfontsize = 8, legend =:none, size = (600,600), c=:black, right_margin = 5Plots.mm, left_margin = 2Plots.mm, ) @@ -55,5 +54,5 @@ gr() # Export figures # savefig(fig2d, joinpath("..", "article", "figures", "fig2d_misplaced")) -savefig(fig2d_flip, joinpath("..", "article", "figures", "fig2d")) +savefig(fig2d_flip, joinpath("..", "article", "figures", "fig2d.pdf")) # savefig(fig2d_pyplot, joinpath("..", "article", "figures", "fig2d_pyplot")) diff --git a/code/figure3.jl b/code/figure3.jl index 384231d..8dd9d94 100644 --- a/code/figure3.jl +++ b/code/figure3.jl @@ -15,10 +15,12 @@ plot(sol_serie1, vars = 1, xlim = (0, 500), ylim = (0, 1), c=:black, linewidth=2 u0_serie2 = [0.78, 0.16, 9.9] prob_serie2 = ODEProblem(parameterized_model!, u0_serie2, tspan, p) -sol_serie2 = solve(prob_serie2) +sol_serie2 = solve(prob_serie2, ) -fig3 = plot!(sol_serie2, vars = 1, xlim = (0, 500), ylim = (0, 1), linestyle = :dash, linewidth = 2, - grid=:none, legend = false, xlabel = "time", ylabel = "x", c = :darkgrey, framestyle = :box) +fig3 = plot!(sol_serie2, vars = 1, xlim = (0, 500), ylim = (0, 1), + c = :darkgrey, linestyle = :dash, linewidth = 2, + xlabel = "time", ylabel = "x", guidefontsize = 10, + grid = :none, legend = false, framestyle = :box) ## Export figures -savefig(fig3, joinpath("..", "article", "figures", "fig3")) +savefig(fig3, joinpath("..", "article", "figures", "fig3.pdf")) diff --git a/code/figure4.jl b/code/figure4.jl index c99b9b6..5a03ebb 100644 --- a/code/figure4.jl +++ b/code/figure4.jl @@ -61,7 +61,7 @@ points_maxloc = unique(hcat(B, vec(Zmaxloc)); dims = 1) pts_maxloc = points_maxloc[points_maxloc[:,2] .> 0.00, :] # Fig.4 A) fig4a = scatter(pts_maxloc[:, 1], pts_maxloc[:, 2], - markersize = 1, + markersize = 2, markeralpha = 0.5, xlim = (2.2, 3.2), ylim = (9.5, 13.0), xlabel = "b1", ylabel = "Zmax", legend = false, grid = :none, c = :black, msw = 0.0, msc = :black, @@ -69,7 +69,7 @@ fig4a = scatter(pts_maxloc[:, 1], pts_maxloc[:, 2], ) # Fig.4 B) fig4b = scatter(pts_maxloc[:, 1], pts_maxloc[:, 2], - markersize = 1, + markersize = 2, markeralpha = 0.5, xlim = (3.0, 6.5), ylim = (3.0, 10.0), xticks = 3.0:0.5:6.5, yticks = (3.0:1.0:10.0, string.(3.0:1.0:10.0)), xlabel = "b1", ylabel = "Zmax", legend = false, @@ -78,7 +78,7 @@ fig4b = scatter(pts_maxloc[:, 1], pts_maxloc[:, 2], ) # Fig.4 C) fig4c = scatter(pts_maxloc[:, 1], pts_maxloc[:, 2], - markersize = 1, + markersize = 2, markeralpha = 0.5, xlim = (2.25, 2.6), ylim = (11.4, 12.8), xticks = 2.25:0.05:2.60, yticks = 11.1:0.2:12.8, xlabel = "b1", ylabel = "Zmax", legend = false, @@ -87,12 +87,12 @@ fig4c = scatter(pts_maxloc[:, 1], pts_maxloc[:, 2], ) # Fig.4 - Combine A,B,C fig4 = plot(fig4a, fig4b, fig4c, layout = (3, 1), - size = (500, 900), titlefontsize = 15, - tickfontsize = 15, guidefontsize = 15, + size = (500, 900), titlefontsize = 11, + tickfontsize = 8, guidefontsize = 10, left_margin = 10Plots.mm, right_margin = 5Plots.mm, bottom_margin = 2Plots.mm, framestyle = :box ) ## Export figures -savefig(fig4, joinpath("..", "article", "figures", "fig4")) +savefig(fig4, joinpath("..", "article", "figures", "fig4.pdf")) diff --git a/code/figure5.jl b/code/figure5.jl index b0c2df3..3282fde 100644 --- a/code/figure5.jl +++ b/code/figure5.jl @@ -142,7 +142,7 @@ plot!(xmin:0.01:xmax, xmin:0.01:xmax, color = :black) # Export complete fig5 fig5 = plot(fig5a, fig5b, fig5c, fig5d, layout = 4, - titlefontsize = 10, + titlefontsize = 11, tickfontsize = 8, guidefontsize = 10, framestyle = :box ) -savefig(fig5, joinpath("..", "article", "figures", "fig5")) +savefig(fig5, joinpath("..", "article", "figures", "fig5.pdf")) diff --git a/code/figureS1.jl b/code/figureS1.jl index f7e5c2f..d085613 100644 --- a/code/figureS1.jl +++ b/code/figureS1.jl @@ -76,11 +76,11 @@ function b2_behavior(;b1val::Float64, b2low::Float64=1.5, b2up::Float64=3.2,out: end # Plot results (bifurcation diagram) scatter(results[:,1], results[:,2], - markersize = 1, + markersize = 1, c = :black, xlabel = "b2", xlim = (b2low,b2up), xticks = b2low:0.25:b2up, ylabel = "Zmax", yticks = (0.0:2.0:maximum(results[:, 2]), string.(0.0:2.0:maximum(results[:, 2]))), legend = false, grid = :none, framestyle = :box, - c = :black) + guidefontsize = 10) end # Examine behavior when changing b2 at b1 = 3.0 @@ -89,7 +89,7 @@ figS1_maxloc = b2_behavior(b1val = 3.0, b2low = 1.5, b2up = 3.2, figS1_all = b2_behavior(b1val = 3.0, out = "all") ## Export figures -savefig(figS1_maxloc, joinpath("..", "article", "figures", "figS1")) +savefig(figS1_maxloc, joinpath("..", "article", "figures", "figS1.pdf")) # Additionnal examinations b2_behavior(b1val = 2.0)