notebooks/relationships_change_dcnt_values.ipynb

{
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Adding optional relationships changes the *dcnt* value\n",
    "**SYNOPSIS**: For GO:0019012, *virion*, the descendants count *dcnt*, is:\n",
    "  * 0 when using *is_a* relationships (the default) and \n",
    "  * 48 when adding the optional relationship, *part_of*.\n",
    "\n",
    "**Table of Contents:**    \n",
    "  1. Download Ontologies, if necessary\n",
    "  2. Depth-01 term, virion, has dcnt=0 through ***is_a*** relationships (default)\n",
    "  3. Depth-01 term, virion, dcnt value is higher using **all** relationships\n",
    "  4. Depth-01 term, virion, dcnt value is higher using ***part_of*** relationships\n",
    "  5. Descendants under virion\n",
    "  6. Plot some descendants of virion"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1) Download Ontologies, if necessary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  EXISTS: go-basic.obo\n",
      "go-basic.obo: fmt(1.2) rel(2019-06-10) 47,442 GO Terms; optional_attrs(relationship)\n"
     ]
    }
   ],
   "source": [
    "from goatools.base import get_godag\n",
    "godag = get_godag(\"go-basic.obo\", optional_attrs={'relationship'})\n",
    "go_leafs = set(o.item_id for o in godag.values() if not o.children)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2) Depth-01 term, GO:0019012 (*virion*) has *dcnt=0* through *is_a* relationships (default)\n",
    "GO:0019012, *virion*, has no GO terms below it through the *is_a* relationship, so the default value of dcnt will be zero, even though it is very high in the DAG at depth=01."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "virion = 'GO:0019012'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INITIALIZING GoSubDag: 27482 sources in 44990 GOs rcnt(True). 0 alt GO IDs\n",
      "             GoSubDag: namedtuple fields: NS level depth GO alt GO_name dcnt D1 id\n",
      "             GoSubDag: relationships: set()\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "gosubdag_r0 = GoSubDag(go_leafs, godag)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Notice that ***dcnt=0*** for GO:0019012, *virion*, even though it is very high in the DAG hierarchy (depth=1). This is because there are no GO IDs under GO:0019012 (*virion*) using the *is_a* relationship."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NtGo(NS='CC', level=1, depth=1, GO='GO:0019012', alt='', GO_name='virion', dcnt=0, D1='T', id='GO:0019012')\n",
      "THE VALUE OF dcnt IS: 0\n"
     ]
    }
   ],
   "source": [
    "nt_virion = gosubdag_r0.go2nt[virion]\n",
    "print(nt_virion)\n",
    "print('THE VALUE OF dcnt IS: {dcnt}'.format(dcnt=nt_virion.dcnt))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3) Depth-01 term, GO:0019012 (*virion*) *dcnt* value is higher using all relationships\n",
    "Load all relationships into GoSubDag using *relationships=True*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INITIALIZING GoSubDag: 27482 sources in 44990 GOs rcnt(True). 0 alt GO IDs\n",
      "             GoSubDag: namedtuple fields: NS level depth reldepth GO alt GO_name dcnt D1 childcnt REL REL_short rel id\n",
      "             GoSubDag: relationships: {'part_of', 'negatively_regulates', 'positively_regulates', 'regulates'}\n"
     ]
    }
   ],
   "source": [
    "gosubdag_r1 = GoSubDag(go_leafs, godag, relationships=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NtGo(NS='CC', level=1, depth=1, reldepth=1, GO='GO:0019012', alt='', GO_name='virion', dcnt=48, D1='Q', childcnt=0, REL='....', REL_short='', rel='p...', id='GO:0019012')\n",
      "THE VALUE OF dcnt IS: 48\n"
     ]
    }
   ],
   "source": [
    "nt_virion = gosubdag_r1.go2nt[virion]\n",
    "print(nt_virion)\n",
    "print('THE VALUE OF dcnt IS: {dcnt}'.format(dcnt=nt_virion.dcnt))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4) Depth-01 term, GO:0019012 (*virion*) *dcnt* value is higher using part_of relationships\n",
    "Load all relationships into GoSubDag using *relationships={'part_of'}*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INITIALIZING GoSubDag: 27482 sources in 44990 GOs rcnt(True). 0 alt GO IDs\n",
      "             GoSubDag: namedtuple fields: NS level depth reldepth GO alt GO_name dcnt D1 childcnt REL REL_short rel id\n",
      "             GoSubDag: relationships: {'part_of'}\n"
     ]
    }
   ],
   "source": [
    "gosubdag_partof = GoSubDag(go_leafs, godag, relationships={'part_of'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NtGo(NS='CC', level=1, depth=1, reldepth=1, GO='GO:0019012', alt='', GO_name='virion', dcnt=48, D1='Q', childcnt=0, REL='.', REL_short='', rel='p', id='GO:0019012')\n",
      "THE VALUE OF dcnt IS: 48\n"
     ]
    }
   ],
   "source": [
    "nt_virion = gosubdag_partof.go2nt[virion]\n",
    "print(nt_virion)\n",
    "print('THE VALUE OF dcnt IS: {dcnt}'.format(dcnt=nt_virion.dcnt))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 5) Descendants under GO:0019012 (*virion*)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "48 descendants of virion were found\n"
     ]
    }
   ],
   "source": [
    "virion_descendants = gosubdag_partof.rcntobj.go2descendants[virion]\n",
    "print('{N} descendants of virion were found'.format(N=len(virion_descendants)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 6) Plot descendants of *virion*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CC GO:0098032 dcnt(0) D-04 icosahedral viral capsid, collar fiber\n",
      "CC GO:0098033 dcnt(0) D-04 icosahedral viral capsid, neck fiber\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.plot.gosubdag_plot import GoSubDagPlot\n",
    "\n",
    "# Limit plot of descendants to get a smaller plot\n",
    "virion_capsid_fiber = {'GO:0098033', 'GO:0098032'}\n",
    "nts = gosubdag_partof.prt_goids(virion_capsid_fiber, \n",
    "                         '{NS} {GO} dcnt({dcnt}) D-{depth:02} {GO_name}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INITIALIZING GoSubDag:   2 sources in  11 GOs rcnt(True). 0 alt GO IDs\n",
      "             GoSubDag: namedtuple fields: NS level depth reldepth GO alt GO_name dcnt D1 childcnt REL REL_short rel id\n",
      "             GoSubDag: relationships: {'part_of'}\n",
      "    2 usr  11 GOs  WROTE: virion_capsid_fiber.png\n"
     ]
    }
   ],
   "source": [
    "# Limit plot size by choosing just two virion descendants\n",
    "# Get a subset containing only a couple virion descendants and their ancestors\n",
    "pltdag = GoSubDag(virion_capsid_fiber, godag, relationships={'part_of'})\n",
    "pltobj = GoSubDagPlot(pltdag)\n",
    "pltobj.plt_dag('virion_capsid_fiber.png')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The descendant count is the number next to the **d** in the GO term boxes.     \n",
    "\n",
    "The **c0** seen in some boxes, like GO:0019012 *virion*, indicates that this term has no children through the default *is_a* relationship, but does have children when viewed using additional optional relationships.    \n",
    "\n",
    "<img src=\"images/virion_capsid_fiber.png\" width=\"650pt\">"
   ]
  }
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