9-advanced-examples.ipynb

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    "import dinkum\n",
    "from dinkum.vfg import Gene, Receptor\n",
    "from dinkum.vfn import Tissue\n",
    "\n",
    "from dinkum.display import MultiTissuePanel, tc_record_activity"
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    "# More advanced functionality\n",
    "\n",
    "For those who want to do more programming... dinkum is written in Python and you can access a lot of the internals. It's not super convenient though!"
   ]
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    "## Accessing tissue/gene activity programmatically\n",
    "\n",
    "Here's an example where we directly access the gene states by tissue and timepoint."
   ]
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      "initializing: dinkum v0.3.2\n",
      "start=1 stop=5\n",
      "t=1\n",
      "\ttissue=M, ['X=1']\n",
      "t=2\n",
      "\ttissue=M, ['X=1', 'Y=0']\n",
      "t=3\n",
      "\ttissue=M, ['X=1', 'Y=1']\n",
      "t=4\n",
      "\ttissue=M, ['X=1', 'Y=1']\n",
      "t=5\n",
      "\ttissue=M, ['X=1', 'Y=1']\n",
      "False\n",
      "True\n"
     ]
    }
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   "source": [
    "dinkum.reset()\n",
    "\n",
    "x = Gene(name='X')\n",
    "y = Gene(name='Y')\n",
    "m = Tissue(name='M')\n",
    "\n",
    "x.is_present(where=m, start=1)\n",
    "\n",
    "# now define a regulatory relationship!\n",
    "y.activated_by(source=x, delay=2)\n",
    "\n",
    "# run for 5 ticks (1 to 5)\n",
    "gene_names = dinkum.vfg.get_gene_names()\n",
    "tissue_names = dinkum.vfn.get_tissue_names()\n",
    "\n",
    "states, tissues, is_active_fn = tc_record_activity(start=1, stop=5, gene_names=gene_names, verbose=True)\n",
    "\n",
    "mp = MultiTissuePanel(states=states, tissue_names=tissue_names, genes_by_name=gene_names)\n",
    "mp.draw(is_active_fn)\n",
    "\n",
    "## access individual tissue/time activity\n",
    "tissue_name = 'M'\n",
    "timepoint = 't=1'\n",
    "gene_name = 'Y'\n",
    "print(is_active_fn(tissue_name, timepoint, gene_name))\n",
    "\n",
    "tissue_name = 'M'\n",
    "timepoint = 't=5'\n",
    "gene_name = 'Y'\n",
    "print(is_active_fn(tissue_name, timepoint, gene_name))"
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