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updated figure 4
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@SamiralVdB
SamiralVdB committed Jul 22, 2024
1 parent 5f02af7 commit 9e985a1
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Binary file removed Figure3_sensitivities_protein-overproduction.png
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82 changes: 46 additions & 36 deletions Figures/Figure3_sensitivities_protein-overproduction.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -230,7 +238,7 @@
},
{
"cell_type": "code",
"execution_count": 49,
"execution_count": 7,
"id": "cf73a888-2270-4ea9-9cc8-4c9e0f5eceaa",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -306,7 +314,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": 8,
"id": "f1fc7967-5869-4911-8ed4-2cee897adbd7",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -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,
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"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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -1222,16 +1230,18 @@
},
{
"cell_type": "code",
"execution_count": 50,
"execution_count": 31,
"id": "8ce6c775-f714-4534-91ce-9c4cfd4e73c2",
"metadata": {},
"outputs": [
{
"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"
]
},
{
Expand Down Expand Up @@ -1293,20 +1303,20 @@
"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": [
{
"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"
]
},
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},
{
"cell_type": "code",
"execution_count": 52,
"execution_count": 33,
"id": "44a1ed1c",
"metadata": {},
"outputs": [
{
"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"
]
},
Expand Down Expand Up @@ -1443,7 +1453,7 @@
},
{
"cell_type": "code",
"execution_count": 42,
"execution_count": 35,
"id": "b13a70c0-e06b-4746-a620-7308de72b7b7",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -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')"
]
},
{
Expand All @@ -1500,15 +1510,15 @@
},
{
"cell_type": "code",
"execution_count": 41,
"execution_count": 37,
"id": "14fe29c7-81a3-4a80-84f4-19d90375ef08",
"metadata": {},
"outputs": [
{
"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"
]
},
Expand Down Expand Up @@ -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"
]
},
{
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