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Sources: json or newick\n* Zoom & Pan\n* Display branch lengths or not\n* Circular or linear layout\n* Metadata on nodes, branches and labels (size, color)\n* Display pies on nodes\n* Collapse nodes\n\n## Browse the tree\n\n* Zoom with the mouse wheel\n* Drag & drop to move into the tree\n* Hover a node or a label to increase its size\n\n## Import in a .vue file\n\n```javascript\nimport { VuePhylogram } from 'vue-phylogram';\n```\n\n## Data Sources\n\nThe following tree can be represented by two formats : newick or json object.\n\n![Simple tree](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/simpleExample.png)\n\n### From newick\n\n```html\n<Phylogram :newick=\"newick\"></Phylogram>\n```\n\n```javascript\n data () {\n    return {\n  newick : \"(((A:0.2, B:0.3):0.3,(C:0.5, D:0.3):0.2):0.3, E:0.7):1.0\"\n  ....\n```\n\n### From Json String\n\nBe careful, after the version 2.1.2, inputTree is not an object anymore but a String.\n\n```html\n<Phylogram :inputTree=\"tree\"></Phylogram>\n```\n\nEach node can have these attributes :\n\n* id : if not, will be computed. Be careful, to map metadata on nodes, they must have an id.\n* name : if not, the node label won't be displayed.\n* length : the length of the branch before the node. If not, the length will be 0.\n* branchset : the list of the nodes starting from this node. If absent, the node will be a leaf of the tree.\n\n```javascript\n data () {\n    return {\n  tree: `{\n        \"id\": \"ABCDE\",\n        \"branchset\": [\n          {\n            \"id\": \"ABCD\",\n            \"length\": 0.2,\n            \"branchset\": [\n              {\n                \"length\": 0.3,\n                \"id\": \"AB\",\n                \"name\": \"AB\",\n                \"branchset\": [\n                  {\n                    \"name\": \"A\",\n                    \"id\": \"A\",\n                    \"length\": 0.2\n                  },\n                  {\n                    \"id\": \"B\",\n                    \"name\": \"B\",\n                    \"length\": 0.3\n                  }\n                ]\n              },\n              {\n                \"length\": 0.2,\n                \"id\": \"CD\",\n                \"name\": \"CD\",\n                \"branchset\": [\n                  {\n                    \"id\": \"C\",\n                    \"name\": \"C\",\n                    \"length\": 0.5\n                  },\n                  {\n                    \"id\": \"D\",\n                    \"name\": \"D\",\n                    \"length\": 0.3\n                  }\n                ]\n              }\n            ]\n          },\n          {\n            \"id\": \"E\",\n            \"name\": \"E\",\n            \"length\": 0.7\n          }\n        ]\n      }`\n  ....\n```\n\n## Generic layout\n\nThese props set up the generic layout :\n\n* width (default : 600)\n* height (default : 400)\n* margin (default : {top:10, right;10, bottom:10, left:10})\n* labelWidth : space allowed to display the labels (default : 200)\n\n##  Display a cladogram or a phylogram\n\nA cladogram does not represent the branch lengths instead of the phylogram.\n\n### Display a phylogram (default)\n\n![Phylogram](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/phylogram.png)\n\n```html\n<Phylogram :newick=\"newick\"></Phylogram>\n```\n\nor\n\n```html\n<Phylogram :newick=\"newick\" :branch-lengths=\"true\" ></Phylogram>\n```\n\nor\n\n```html\n<Phylogram :newick=\"newick\" branch-lengths ></Phylogram>\n```\n\n### Display a cladogram\n\n![Cladogram](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/cladogram.png)\n\n```html\n<Phylogram :newick=\"newick\" :branch-lengths=\"false\" ></Phylogram>\n```\n\n## Display tree with right or smooth angles\n\n### Display tree with right angles (default)\n\n```html\n<Phylogram :newick=\"newick\" right-angle></Phylogram>\n```\n\n```html\n<Phylogram :newick=\"newick\" :right-angle=\"true\" ></Phylogram>\n```\n\n### Display tree with smooth angles\n\n![Smooth Phylogram](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/phylogramSmooth.png)\n\n```html\n<Phylogram :newick=\"newick\" :right-angle=\"false\" ></Phylogram>\n```\n\n## Circular layout\n\n![Circular](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/circular.png)\n\nBy default, the tree is displayed in a linear way. If you want to display the tree as a circle:\n\n```html\n<Phylogram :newick=\"newick\" circular ></Phylogram>\n```\n\n## Display leaves\n\nLeaves are displayed by default. To hide them:\n\n```html\n<Phylogram :newick=\"newick\" :display-leaves=\"false\" ></Phylogram>\n```\n\n## Display inner nodes\n\nInner nodes are hiddent by default. To show them:\n\n```html\n<Phylogram :newick=\"newick\" :display-inner-nodes=\"true\" ></Phylogram>\n```\n\n##  Display leaf labels\n\nThe leaf labels are displayed by default. To hide them:\n\n```html\n<Phylogram :newick=\"newick\" :display-leaf-labels=\"false\" ></Phylogram>\n```\n\n## Display inner labels\n\nThe inner labels are hidden by default. To show them:\n\n```html\n<Phylogram :newick=\"newick\" :display-inner-labels=\"true\" ></Phylogram>\n```\n\n## Align labels\n\nBy default, labels are displayed close to the nodes. If you want to right align them :\n\n```html\n<Phylogram :newick=\"newick\" align-labels ></Phylogram>\n```\n\n## Space for labels\n\nIf you want to increase or reduce the width of the space assigned to the labels, use the label-width prop:\n\n```html\n<Phylogram :newick=\"newick\" :label-width=400 ></Phylogram>\n```\n\n## Display support values\n\nSupport values (e.g bootstrap values) can be read from newick string following the two ways described [here]([https://link](https://www.megasoftware.net/mega4/WebHelp/glossary/rh_newick_format.htm).\n\nIn the json object, the source node must have a key called \"support\":\n\n```json\n\"branchset\": [\n  {\n    \"id\": \"ABCD\",\n    \"support\":85,\n    \"length\": 0.2,\n    \"branchset\": [\n      {\n        \"length\": 0.3,\n        \"id\": \"AB\",\n        \"support\":90,\n        \"name\": \"AB\",\n        \"branchset\": [\n        ...\n```\n\n## Metadata\n\n### Branch colors\n\n![Color branches](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/colorBranches.png)\n\nDefault branch colors can be set with the **defaultColors** props:\n\n```html\n<Phylogram :inputTree=\"tree\" :default-colors=\"defaultColors\">\n```\n\n```json\ndefaultColors: {\n  branch: 'grey',\n  selected_branch: 'yellow'\n}\n```\n\nColors for specific branches can also be set with the **branchStyles** props.\n\n```html\n<Phylogram :inputTree=\"tree\" :branch-styles=\"branchStyles\">\n```\n\nThe branches are identified by the node that they reach (type:'to') or that they start from (type:'from') or both (type:'both') (default)\n\n```json\nbranchStyles: {\n  CD: {\n    color: 'green',\n    type: 'from'\n  },\n  ABCD: {\n    color: 'orange',\n    type: 'to'\n  },\n  AB: {\n    color: 'brown',\n    type: 'both'\n  }\n}\n```\n\n### Node styles\n\n![Node Styles](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/nodeStyles.png)\n\nDefault fill and outline node colors can be set with the **defaultColors** props.\n\n```html\n<Phylogram :inputTree=\"tree\" :branch-styles=\"branchStyles\">\n```\n\n```json\ndefaultColors:{\n  \"leaf_fill\":\"#B0C4DE\",\n  \"inner_fill\":\"#6495ED\",\n  \"root_fill\":\"#32CD32\",\n  \"selected_fill\":\"#B22222\",\n  \"leaf_stroke\":\"#4682B4\",\n  \"inner_stroke\":\"#4169E1\",\n  \"root_stroke\":\"#556B2F\",\n  \"selected_stroke\":\"#FF0000\"\n}\n```\n\nSize and color can be set for each leaf node with the **nodeStyles** props.\n\n```html\n<Phylogram :inputTree=\"tree\" :node-styles=\"nodeStyles\">\n```\n\n```json\nnodeStyles: {\n    C: {\n      size: 3,\n      fill: 'orange'\n    },\n    B: {\n      size: 0.5,\n      stroke: 'red'\n    }\n  }\n}\n```\n\n### Label styles\n\n```html\n<Phylogram :inputTree=\"tree\" :label-styles=\"labelStyles\">\n```\n\nDefault colors for all labels and labels of selected nodes are configurable in the defaultColors prop:\n\n```json\ndefaultColors: {\n  label_color: 'black',\n  selected_label_color: 'red'\n}\n```\n\nBackground, border and stroke colors can also be set for each label.\n\n![Label Styles](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/labelStyles.png)\n\n```html\n<Phylogram :inputTree=\"tree\" :label-styles=\"labelStyles\">\n```\n\n```json\nlabelStyles: {\n  A: {\n    color: 'orange',\n    background: 'darkgreen',\n    borderWidth: 2\n  },\n  C: {\n    background: 'yellow'\n  },\n  D: {\n    borderWidth: 1\n  },\n  E: {\n    borderWidth: 4,\n    borderColor: 'red'\n  }\n}\n```\n\n### Display pies on nodes\n\n![Pies](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/pies.png)\n\nHover a part of the pie to display the corresponding values.\n\n```html\n<Phylogram :inputTree=\"tree\" :pies=\"pies\">\n```\n\nBe careful, the ids of the nodes must be well specified.\n\n```json\npies: {\n  A: {\n    data: [\n      { label: 'value 1', value: 10, color: 'blue' },\n      { label: 'value 2', value: 20, color: 'green' },\n      { label: 'value 3', value: 30, color: 'red' }\n    ],\n    size: 5\n  },\n  ABCD: {\n    data: [\n      { label: 'value 1', value: 50, color: 'blue' },\n      { label: 'value 2', value: 80, color: 'green' },\n      { label: 'value 3', value: 50, color: 'red' }\n    ],\n    size: 3\n  },\n  CD: {\n    data: [\n      { label: 'value 1', value: 90, color: 'blue' },\n      { label: 'value 2', value: 10, color: 'green' }\n    ],\n    size: 10\n  }\n}\n```\n\nIf you want to hide pies :\n\n```html\n<Phylogram :inputTree=\"tree\" :pies=\"pies\" :show-pies=\"false\">\n```\n\n### Display glyphs beside leaves\n\n![Pies](https://raw.githubusercontent.com/lipme/vue-phylogram/master/public/images/glyphs.png)\n\n```html\n<Phylogram :inputTree=\"tree\" :glyphs=\"glyphs\">\n```\n\nThe glyphs must be an array with this format :\n\n```json\nglyphs: [\n  {\n    label: 'Good/Bad',\n    categories: [\n      {\n        label: 'good',\n        style: { fill: 'green' },\n        ids: ['A', 'C']\n      },\n      {\n        label: 'bad',\n        style: { fill: 'red' },\n        ids: ['D', 'E']\n      }\n    ]\n  },\n  {\n    label: 'Yes/No',\n    categories: [\n      {\n        label: 'yes',\n        style: { fill: 'cyan' },\n        ids: ['B']\n      },\n      {\n        label: 'no',\n        style: { fill: 'purple' },\n        ids: ['A', 'E']\n      }\n    ]\n  }\n]\n```\n\nIf you want do hide glyphs:\n\n```html\n<Phylogram :inputTree=\"tree\" :glyphs=\"glyphs\" :show-glyphs=\"false\">\n```\n\nIf you don't want that a tooltip is displayed when a glyph is hovered:\n\n```html\n<Phylogram :inputTree=\"tree\" :glyphs=\"glyphs\" :show-glyph-labels=\"false\">\n```\n\nIf you want to add margin between each glyph:\n```html\n<Phylogram :inputTree=\"tree\" :glyphs=\"glyphs\" glyph-margin=\"5\">\n```\n\n## Select nodes from props\n\nUse the \"selected\" props and put the node ids separateb by commas.\n\n```html\n<Phylogram :inputTree=\"tree\" :selected=\"AB,E\">\n```\n\n## Collapse nodes from props\n\nUse the \"selected\" props and put the node ids separateb by commas.\n\n```html\n<Phylogram :inputTree=\"tree\" :collapsed=\"AB,CD\">\n```\n\n## Layout mode\n\nBy default, branches are not ordered (layout-mode=0)\nTo sort the branches by ascending length:\n\n```html\n<Phylogram :inputTree=\"tree\" :layout-mode=\"1\">\n```\n\nTo sort the branches by descending length:\n\n```html\n<Phylogram :inputTree=\"tree\" :layout-mode=\"2\">\n```\n\n## Events\n\n* select-nodes: when the user selects or deselect one node, returns the array of the selected node ids.\n\n* collapse-nodes: when the user collapses a node or uncollapse a node, returns the array of the collapsed node ids.\n\n* click-node\n* right-click-node\n* hover-node\n* click-outside : click outside the nodes\n* click-label\n* right-click-label\n* hover-label\n\n## Project setup\n\n```console\nnpm install\n```\n\n### Compiles and hot-reloads for development\n\n```console\nnpm run serve\n```\n\n### Compiles and minifies for production\n\n```console\nnpm run build\n```\n\n### Run your unit tests\n\n```console\nnpm run test:unit\n```\n\n### Lints and fixes files\n\n```console\nnpm run lint\n```\n\n### Customize configuration\n\nSee [Configuration Reference](https://cli.vuejs.org/config/).\n","readmeFilename":"README.md"}