Add in vivo concentrations figure

Author: Paulocracy

cosa/in_vivo_concentrations_figure.png

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+import matplotlib.pyplot as plt
+import pandas
+from helper import json_load
+
+def create_in_vivo_concentrations_figure():
+    ratio_ratio_test_data_aerobic = json_load("cosa/results_aerobic/ratio_ratio_test_data.json")
+    concentration = "VIVOCONC"
+    target = "OPTSUBMDF"
+
+    figurename_tuple = ("aerobic", f"2C_NADH_to_NAD___to___NADPH_to_nadp_{target}_{concentration}.jpg")
+
+    fig, axs = plt.subplots(nrows=2, ncols=1, dpi=500, figsize=(6, 8)) #sharex=True, figsize=(50, 25), dpi=120, facecolor="white")
+    fig.tight_layout(pad=3.75)
+
+    ########################################################
+    ########################################################
+    ########################################################
+    # 0: Random sampling figure
+    str_to_float = lambda x: float(x.replace(",", "."))
+    list_to_float = lambda x: [str_to_float(y) for y in x]
+
+    growth_rate_id = "µ [1/h]"
+    best_id = "FLEXIBLE"
+    in_vivo_id = "WILDTYPE"
+    only_one_id = "SINGLE_COFACTOR"
+
+    table_path = f"cosa/results_aerobic/optsubmdf_table_VIVOCONC.csv"
+    table = pandas.read_csv(
+        table_path,
+        sep="\t",
+    )
+
+    headers = list(table.keys())
+    del(headers[headers.index(best_id)])
+    del(headers[headers.index(only_one_id)])
+    del(headers[headers.index(in_vivo_id)])
+    headers += [only_one_id, in_vivo_id, best_id]
+
+    growth_rates = list_to_float(table[growth_rate_id])
+    is_first_random = True
+    for header in headers:
+        if header == growth_rate_id:
+            continue
+        elif header == best_id:
+            label = "Flexible specificity"
+            linestyle = "--"
+            color = "yellowgreen"
+            linewidth = 2.0
+        elif header == in_vivo_id:
+            label = "Wild-type specificity"
+            linestyle = "-"
+            color = "black"
+            linewidth = 2.0
+        elif header == only_one_id:
+            label = "Single cofactor pool"
+            linestyle = "-"
+            color = "red"
+            linewidth = 2.0
+        else:
+            if is_first_random:
+                label = "Random specificities"
+                is_first_random = False
+            else:
+                label = ""
+            linestyle = "-"
+            color = "paleturquoise"
+            linewidth = 1.0
+
+        axs[0].plot(
+            growth_rates[:11], # x
+            list_to_float(table[header])[:11], # y
+            label=label,
+            linestyle=linestyle,
+            color=color,
+            linewidth=linewidth,
+        )
+    axs[0].legend(loc="lower left")
+    axs[0].set_title("A", loc="left", fontweight="bold")
+    axs[0].set_xlabel("Growth rate [1/h]")
+    axs[0].set_ylabel("OptSubMDF [kJ/mol]")
+    axs[0].set_xlim(min(growth_rates[:11]), max(growth_rates[:11]))
+
+
+    ########################################################
+    ########################################################
+    ########################################################
+    # 1: Ratio ratio figure
+    ratio_ratio_test_data = ratio_ratio_test_data_aerobic
+
+    min_label = "Minimal ratio"
+    max_label = "Maximal ratio"
+
+    figurename = figurename_tuple[1]
+    plotted_growth_rates = ratio_ratio_test_data[figurename]["plotted_growth_rates"][:10]
+    min_ratios = ratio_ratio_test_data[figurename]["min_ratios"][:10]
+    max_ratios = ratio_ratio_test_data[figurename]["max_ratios"][:10]
+    axs[1].plot(
+        plotted_growth_rates[::-1], # x
+        min_ratios[::-1], # y
+        "bo",
+        label=min_label,
+        linewidth=1.0,
+    )
+    axs[1].plot(
+        plotted_growth_rates[::-1], # x
+        max_ratios[::-1], # y
+        "ro",
+        label=max_label,
+        linewidth=1.0,
+    )
+    axs[1].legend(loc="upper center", ncol=2)
+    axs[1].set_title("B", loc="left", fontweight="bold")
+    axs[1].set_ylim(-.0005, 0.01)
+    axs[1].set_xlabel("Growth rate [1/h]")
+    axs[1].set_ylabel(r"$\mathrm{\frac{[NADH]/[NAD^{+}]}{[NADPH]/[NADP^{+}]}}$", fontsize=13)
+
+    fig.savefig(f"./cosa/in_vivo_concentrations_figure.png", bbox_inches='tight', pad_inches=0.05)
+    plt.close()
+
+create_in_vivo_concentrations_figure()