diff --git a/Figure3_sensitivities_protein-overproduction.png b/Figure3_sensitivities_protein-overproduction.png deleted file mode 100644 index 2396ef4..0000000 Binary files a/Figure3_sensitivities_protein-overproduction.png and /dev/null differ diff --git a/Figures/Figure3_sensitivities_protein-overproduction.ipynb b/Figures/Figure3_sensitivities_protein-overproduction.ipynb index f096783..37fb141 100644 --- a/Figures/Figure3_sensitivities_protein-overproduction.ipynb +++ b/Figures/Figure3_sensitivities_protein-overproduction.ipynb @@ -11,10 +11,18 @@ }, { "cell_type": "code", - "execution_count": 40, + "execution_count": 1, "id": "3e02abee-b41a-4257-ae81-9f22b71d17b3", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loading PAModelpy modules version 0.0.3.3\n" + ] + } + ], "source": [ "from matplotlib import pyplot as plt\n", "import matplotlib\n", @@ -230,7 +238,7 @@ }, { "cell_type": "code", - "execution_count": 49, + "execution_count": 7, "id": "cf73a888-2270-4ea9-9cc8-4c9e0f5eceaa", "metadata": {}, "outputs": [], @@ -306,7 +314,7 @@ }, { "cell_type": "code", - "execution_count": 38, + "execution_count": 8, "id": "f1fc7967-5869-4911-8ed4-2cee897adbd7", "metadata": {}, "outputs": [], @@ -424,26 +432,26 @@ { "data": { "text/plain": [ - "{'leu__L_c': 0.08130081300813008,\n", - " 'cys__L_c': 0.008130081300813009,\n", - " 'ala__L_c': 0.036585365853658534,\n", - " 'thr__L_c': 0.06097560975609756,\n", - " 'glu__L_c': 0.06910569105691057,\n", - " 'gln__L_c': 0.032520325203252036,\n", - " 'gly_c': 0.09349593495934959,\n", - " 'tyr__L_c': 0.044715447154471545,\n", - " 'lys__L_c': 0.08130081300813008,\n", + "{'trp__L_c': 0.0040650406504065045,\n", + " 'asp__L_c': 0.07317073170731707,\n", " 'val__L_c': 0.06910569105691057,\n", - " 'asn__L_c': 0.052845528455284556,\n", - " 'trp__L_c': 0.0040650406504065045,\n", - " 'ser__L_c': 0.032520325203252036,\n", " 'pro__L_c': 0.04065040650406504,\n", - " 'phe__L_c': 0.052845528455284556,\n", - " 'his__L_c': 0.06504065040650407,\n", " 'met__L_c': 0.024390243902439025,\n", - " 'asp__L_c': 0.07317073170731707,\n", + " 'phe__L_c': 0.052845528455284556,\n", + " 'leu__L_c': 0.08130081300813008,\n", + " 'ile__L_c': 0.04878048780487805,\n", + " 'glu__L_c': 0.06910569105691057,\n", " 'arg__L_c': 0.028455284552845527,\n", - " 'ile__L_c': 0.04878048780487805}" + " 'ser__L_c': 0.032520325203252036,\n", + " 'lys__L_c': 0.08130081300813008,\n", + " 'asn__L_c': 0.052845528455284556,\n", + " 'ala__L_c': 0.036585365853658534,\n", + " 'cys__L_c': 0.008130081300813009,\n", + " 'gly_c': 0.09349593495934959,\n", + " 'gln__L_c': 0.032520325203252036,\n", + " 'tyr__L_c': 0.044715447154471545,\n", + " 'thr__L_c': 0.06097560975609756,\n", + " 'his__L_c': 0.06504065040650407}" ] }, "execution_count": 13, @@ -510,7 +518,7 @@ "text": [ "Set parameter Username\n", "Academic license - for non-commercial use only - expires 2025-03-06\n", - "Read LP format model from file /tmp/tmprhf0m20b.lp\n", + "Read LP format model from file /tmp/tmpli4k8wpd.lp\n", "Reading time = 0.01 seconds\n", ": 1877 rows, 5424 columns, 21150 nonzeros\n", "Setting up the proteome allocation model iML1515\n", @@ -771,7 +779,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Read LP format model from file /tmp/tmpdpcabaka.lp\n", + "Read LP format model from file /tmp/tmpivebp_ql.lp\n", "Reading time = 0.01 seconds\n", ": 1877 rows, 5424 columns, 21150 nonzeros\n", "Setting up the proteome allocation model iML1515\n", @@ -999,7 +1007,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Read LP format model from file /tmp/tmp516ifhqr.lp\n", + "Read LP format model from file /tmp/tmp4_xmbxls.lp\n", "Reading time = 0.01 seconds\n", ": 1877 rows, 5424 columns, 21150 nonzeros\n", "Setting up the proteome allocation model iML1515\n", @@ -1222,7 +1230,7 @@ }, { "cell_type": "code", - "execution_count": 50, + "execution_count": 31, "id": "8ce6c775-f714-4534-91ce-9c4cfd4e73c2", "metadata": {}, "outputs": [ @@ -1230,8 +1238,10 @@ "name": "stderr", "output_type": "stream", "text": [ - "/tmp/ipykernel_13353/3670735817.py:46: UserWarning: constrained_layout not applied because axes sizes collapsed to zero. Try making figure larger or axes decorations smaller.\n", - " fig.savefig('Figure3_sensitivities_protein-overproduction.png', dpi =200,bbox_inches='tight')\n" + "/tmp/ipykernel_23069/3670735817.py:46: UserWarning: constrained_layout not applied because axes sizes collapsed to zero. Try making figure larger or axes decorations smaller.\n", + " fig.savefig('Figure3_sensitivities_protein-overproduction.png', dpi =200,bbox_inches='tight')\n", + "/usr/lib/python3/dist-packages/IPython/core/pylabtools.py:151: UserWarning: constrained_layout not applied because axes sizes collapsed to zero. Try making figure larger or axes decorations smaller.\n", + " fig.canvas.print_figure(bytes_io, **kw)\n" ] }, { @@ -1293,12 +1303,12 @@ "fig.set_figheight(height)\n", "fig.align_labels()\n", "\n", - "fig.savefig('Figure3_sensitivities_protein-overproduction.png', dpi =200,bbox_inches='tight')" + "# fig.savefig('Figure3_sensitivities_protein-overproduction.png', dpi =200,bbox_inches='tight')" ] }, { "cell_type": "code", - "execution_count": 51, + "execution_count": 32, "id": "7dc9eac9", "metadata": {}, "outputs": [ @@ -1306,7 +1316,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/tmp/ipykernel_13353/2688687879.py:25: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n", + "/tmp/ipykernel_23069/2688687879.py:25: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n", " fig.subplots_adjust(left=0.3)\n" ] }, @@ -1359,7 +1369,7 @@ }, { "cell_type": "code", - "execution_count": 52, + "execution_count": 33, "id": "44a1ed1c", "metadata": {}, "outputs": [ @@ -1367,7 +1377,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/tmp/ipykernel_13353/1010484757.py:24: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n", + "/tmp/ipykernel_23069/1010484757.py:24: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n", " fig.subplots_adjust(left=0.3)\n" ] }, @@ -1443,7 +1453,7 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": 35, "id": "b13a70c0-e06b-4746-a620-7308de72b7b7", "metadata": {}, "outputs": [ @@ -1486,7 +1496,7 @@ "\n", "plt.show()\n", "\n", - "fig.savefig('SuppFigure6_eGFP-normalized_mu.png', dpi =200,bbox_inches='tight')" + "fig.savefig('Figures/SuppFigure6_eGFP-normalized_mu.png', dpi =200,bbox_inches='tight')" ] }, { @@ -1500,7 +1510,7 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": 37, "id": "14fe29c7-81a3-4a80-84f4-19d90375ef08", "metadata": {}, "outputs": [ @@ -1508,7 +1518,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/tmp/ipykernel_13353/3374466483.py:48: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n", + "/tmp/ipykernel_23069/2479724123.py:48: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n", " plt.tight_layout()\n" ] }, @@ -1577,7 +1587,7 @@ "plt.subplots_adjust(wspace=0.2, hspace=0.2)\n", "fig.set_figheight(13)\n", "fig.set_figwidth(10)\n", - "fig.savefig('SuppFigure4_simulated-physiology.png')\n" + "fig.savefig('Figures/SuppFigure4_simulated-physiology.png')\n" ] }, { diff --git a/Figures/SuppFigure4_simulated-physiology.png b/Figures/SuppFigure4_simulated-physiology.png index c53bb04..55bbb26 100644 Binary files a/Figures/SuppFigure4_simulated-physiology.png and b/Figures/SuppFigure4_simulated-physiology.png differ