layouts in py4cytoscsape.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "dc290eae",
   "metadata": {},
   "outputs": [],
   "source": [
    "import py4cytoscape as p4c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "b2ac4205",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "You are connected to Cytoscape!\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'You are connected to Cytoscape!'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.cytoscape_ping()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "3778812b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Sonic Hedgehog']"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_network_list()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "0534b1f9",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "style_name not specified, so accessing \"default\" style.\n",
      "style_name not specified, so accessing \"default\" style.\n",
      "style_name not specified, so accessing \"default\" style.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{}"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def estimate_idealEdgeLength():\n",
    "    dependencies=p4c.get_style_dependencies()\n",
    "    if dependencies.get(\"NodeSizeLocked\") is True:\n",
    "        return int(p4c.get_visual_property_default(\"NODE_SIZE\") * 1.5)\n",
    "    else:\n",
    "        width=p4c.get_visual_property_default(\"NODE_WIDTH\")\n",
    "        height=p4c.get_visual_property_default(\"NODE_HEIGHT\")\n",
    "        return int(max(width,height)*1.5)\n",
    "    \n",
    "p4c.layout_network(layout_name='cose' + \" idealEdgeLength=\" + str(estimate_idealEdgeLength()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "d5bd8da1",
   "metadata": {},
   "outputs": [],
   "source": [
    "USER=\"dexterpratt\"\n",
    "PASSWORD=\"cytoscaperules\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "348d498b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'58a9b283-3ffb-11ec-b3be-0ac135e8bacf'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.export_network_to_ndex(username=USER, password=PASSWORD, is_public=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "7835c4b5",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['attribute-grid',\n",
       " 'degree-circle',\n",
       " 'attributes-layout',\n",
       " 'kamada-kawai',\n",
       " 'force-directed',\n",
       " 'cose',\n",
       " 'hierarchical',\n",
       " 'attribute-circle',\n",
       " 'stacked-node-layout',\n",
       " 'boundary-layout',\n",
       " 'circular',\n",
       " 'grid',\n",
       " 'fruchterman-rheingold',\n",
       " 'isom',\n",
       " 'force-directed-cl']"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_layout_names()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "63c8892d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['spacing', 'singlePartition']"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_layout_property_names(\"attribute-circle\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "d604ddfa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "50"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_layout_property_value(\"cose\", \"idealEdgeLength\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "7aede0db",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['COMPOUND_NODE_PADDING',\n",
       " 'COMPOUND_NODE_SHAPE',\n",
       " 'DING_RENDERING_ENGINE_ROOT',\n",
       " 'EDGE',\n",
       " 'EDGE_BEND',\n",
       " 'EDGE_CURVED',\n",
       " 'EDGE_LABEL',\n",
       " 'EDGE_LABEL_COLOR',\n",
       " 'EDGE_LABEL_FONT_FACE',\n",
       " 'EDGE_LABEL_FONT_SIZE',\n",
       " 'EDGE_LABEL_ROTATION',\n",
       " 'EDGE_LABEL_TRANSPARENCY',\n",
       " 'EDGE_LABEL_WIDTH',\n",
       " 'EDGE_LINE_TYPE',\n",
       " 'EDGE_PAINT',\n",
       " 'EDGE_SELECTED',\n",
       " 'EDGE_SELECTED_PAINT',\n",
       " 'EDGE_SOURCE_ARROW_SELECTED_PAINT',\n",
       " 'EDGE_SOURCE_ARROW_SHAPE',\n",
       " 'EDGE_SOURCE_ARROW_SIZE',\n",
       " 'EDGE_SOURCE_ARROW_UNSELECTED_PAINT',\n",
       " 'EDGE_STACKING',\n",
       " 'EDGE_STACKING_DENSITY',\n",
       " 'EDGE_STROKE_SELECTED_PAINT',\n",
       " 'EDGE_STROKE_UNSELECTED_PAINT',\n",
       " 'EDGE_TARGET_ARROW_SELECTED_PAINT',\n",
       " 'EDGE_TARGET_ARROW_SHAPE',\n",
       " 'EDGE_TARGET_ARROW_SIZE',\n",
       " 'EDGE_TARGET_ARROW_UNSELECTED_PAINT',\n",
       " 'EDGE_TOOLTIP',\n",
       " 'EDGE_TRANSPARENCY',\n",
       " 'EDGE_UNSELECTED_PAINT',\n",
       " 'EDGE_VISIBLE',\n",
       " 'EDGE_WIDTH',\n",
       " 'EDGE_Z_ORDER',\n",
       " 'NETWORK',\n",
       " 'NETWORK_ANNOTATION_SELECTION',\n",
       " 'NETWORK_BACKGROUND_PAINT',\n",
       " 'NETWORK_CENTER_X_LOCATION',\n",
       " 'NETWORK_CENTER_Y_LOCATION',\n",
       " 'NETWORK_CENTER_Z_LOCATION',\n",
       " 'NETWORK_DEPTH',\n",
       " 'NETWORK_EDGE_SELECTION',\n",
       " 'NETWORK_FORCE_HIGH_DETAIL',\n",
       " 'NETWORK_HEIGHT',\n",
       " 'NETWORK_NODE_LABEL_SELECTION',\n",
       " 'NETWORK_NODE_SELECTION',\n",
       " 'NETWORK_SCALE_FACTOR',\n",
       " 'NETWORK_SIZE',\n",
       " 'NETWORK_TITLE',\n",
       " 'NETWORK_WIDTH',\n",
       " 'NODE',\n",
       " 'NODE_BORDER_PAINT',\n",
       " 'NODE_BORDER_STROKE',\n",
       " 'NODE_BORDER_TRANSPARENCY',\n",
       " 'NODE_BORDER_WIDTH',\n",
       " 'NODE_CUSTOMGRAPHICS_1',\n",
       " 'NODE_CUSTOMGRAPHICS_2',\n",
       " 'NODE_CUSTOMGRAPHICS_3',\n",
       " 'NODE_CUSTOMGRAPHICS_4',\n",
       " 'NODE_CUSTOMGRAPHICS_5',\n",
       " 'NODE_CUSTOMGRAPHICS_6',\n",
       " 'NODE_CUSTOMGRAPHICS_7',\n",
       " 'NODE_CUSTOMGRAPHICS_8',\n",
       " 'NODE_CUSTOMGRAPHICS_9',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_1',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_2',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_3',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_4',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_5',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_6',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_7',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_8',\n",
       " 'NODE_CUSTOMGRAPHICS_POSITION_9',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_1',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_2',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_3',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_4',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_5',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_6',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_7',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_8',\n",
       " 'NODE_CUSTOMGRAPHICS_SIZE_9',\n",
       " 'NODE_CUSTOMPAINT_1',\n",
       " 'NODE_CUSTOMPAINT_2',\n",
       " 'NODE_CUSTOMPAINT_3',\n",
       " 'NODE_CUSTOMPAINT_4',\n",
       " 'NODE_CUSTOMPAINT_5',\n",
       " 'NODE_CUSTOMPAINT_6',\n",
       " 'NODE_CUSTOMPAINT_7',\n",
       " 'NODE_CUSTOMPAINT_8',\n",
       " 'NODE_CUSTOMPAINT_9',\n",
       " 'NODE_DEPTH',\n",
       " 'NODE_FILL_COLOR',\n",
       " 'NODE_HEIGHT',\n",
       " 'NODE_LABEL',\n",
       " 'NODE_LABEL_COLOR',\n",
       " 'NODE_LABEL_FONT_FACE',\n",
       " 'NODE_LABEL_FONT_SIZE',\n",
       " 'NODE_LABEL_POSITION',\n",
       " 'NODE_LABEL_ROTATION',\n",
       " 'NODE_LABEL_TRANSPARENCY',\n",
       " 'NODE_LABEL_WIDTH',\n",
       " 'NODE_NESTED_NETWORK_IMAGE_VISIBLE',\n",
       " 'NODE_PAINT',\n",
       " 'NODE_SELECTED',\n",
       " 'NODE_SELECTED_PAINT',\n",
       " 'NODE_SHAPE',\n",
       " 'NODE_SIZE',\n",
       " 'NODE_TOOLTIP',\n",
       " 'NODE_TRANSPARENCY',\n",
       " 'NODE_VISIBLE',\n",
       " 'NODE_WIDTH',\n",
       " 'NODE_X_LOCATION',\n",
       " 'NODE_Y_LOCATION',\n",
       " 'NODE_Z_LOCATION']"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_visual_property_names()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "073e5029",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "style_name not specified, so accessing \"default\" style.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "35.0"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_visual_property_default(\"NODE_SIZE\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "9c923161",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "style_name not specified, so accessing \"default\" style.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'arrowColorMatchesEdge': False,\n",
       " 'nodeCustomGraphicsSizeSync': True,\n",
       " 'nodeSizeLocked': False}"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p4c.get_style_dependencies()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2ffefcf2",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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