21:null 22:["$","title",null,{"children":"PREI Evolutionary imputation validation: | Avery Selberg | Observable"}] 27:[{"id":"4181c944e73328b46e72fc24d18f7df45b1b2d23c8963f69e78b31a679b9e2620907bd3a2b10d17b897fc7d8d393c84d9bf4fdc89cbf8153d720d26424ce8216","href":"https://static.observableusercontent.com/files/4181c944e73328b46e72fc24d18f7df45b1b2d23c8963f69e78b31a679b9e2620907bd3a2b10d17b897fc7d8d393c84d9bf4fdc89cbf8153d720d26424ce8216","name":"11-datasets_after.json","type":"application/json","lastModified":1649949200207.852,"size":449832},{"id":"f316cea1c64ca2670c41c392af2af247e8d715b74b74a1782e77283298267eaccf1ffa7cf515360ffbfcc9de6c6cd6e4c5cf7b8fb0282fbbe49b4e7b76a03e1a","href":"https://static.observableusercontent.com/files/f316cea1c64ca2670c41c392af2af247e8d715b74b74a1782e77283298267eaccf1ffa7cf515360ffbfcc9de6c6cd6e4c5cf7b8fb0282fbbe49b4e7b76a03e1a","name":"11-datasets_after_trees@1.json","type":"application/json","lastModified":1649949200207.852,"size":25943},{"id":"7507527bd4a18d1f7da4b715d8c875e88eef973c3604dbd7d013f8c6b037fd73cb1eedff6488c2f6a758c7f95ca6ef361e6a561403d96f0b36ca82ad903f6229","href":"https://static.observableusercontent.com/files/7507527bd4a18d1f7da4b715d8c875e88eef973c3604dbd7d013f8c6b037fd73cb1eedff6488c2f6a758c7f95ca6ef361e6a561403d96f0b36ca82ad903f6229","name":"11-datasets_b4.json","type":"application/json","lastModified":1649949200207.852,"size":449820}] 25:{"id":"ae7e48cd3947bba9","slug":"prei-evolutionary-imputation-validation/2","title":"PREI Evolutionary imputation validation:","thumbnail":"ceb7d4ef0f13612e66d1324b35a774c55ab0a140ffb55316c04668f2dbbd996a","access_level":"public","create_time":"$D2022-04-14T15:13:20.207Z","update_time":"$D2022-06-22T16:58:05.358Z","view_time":null,"first_public_time":"$D2022-04-14T15:51:26.640Z","has_unpublished_edits":null,"fork":{"id":"d92c4cf9e722943c","slug":"prei-evolutionary-imputation-validation","title":"PREI Evolutionary imputation validation","owner":{"id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg"}},"stars":0,"starred":false,"owner":{"type":"team","id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":"starter_2024"},"version":619,"publish_version":619,"role":null,"authored":false,"authors":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null}],"members":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":3,"collection":null,"type":"notebook","body":{"title":"PREI Evolutionary imputation validation:","cells":[{"id":0,"value":"# PREI Evolutionary imputation validation:\n## Before vs after update","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":250,"value":"\nviewof chosen_dataset = select ({\n \"options\" : [\"adh\", \"bglobin\", \"camelid\", \"ENCenv\" , \"flavNS5\", \"HepatitisD\", \"HIVvif\", \"IAV_Chen\", \"lysin\", \"yokoyama.rh1.cds.mod.1-990\"],\n \"title\" : \"Choose dataset:\"\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":283,"value":"md`### Tree for ${chosen_dataset}\nNote: branch lengths were estimated in hyphy with Global MG94xREV`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":400,"value":"chosen_tree = { \n let chosen_tree = \"\"\n for (let i = 0; i < data_and_trees.length; i++) {\n if (data_and_trees[i].DATASET == chosen_dataset){ \n return chosen_tree = data_and_trees[i].TREE;\n}\n}\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":329,"value":"rendered_tree = tree.render({\n height:600, \n width:600,\n 'left-right-spacing': 'fit-to-size', \n 'top-bottom-spacing': 'fit-to-size'\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":501,"value":"md`#### How branch length affects mean probability for the dataset: ${chosen_dataset}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":436,"value":"Plot.plot({\n y: {\n grid: true,\n inset: 5\n },\n marks: [\n Plot.lineY(reduced_both.sort(function(a, b){return a.BRANCH_LENGTH - b.BRANCH_LENGTH}), {x: \"BRANCH_LENGTH\", y: \"MEAN_PROBABILITY\", stroke: \"B4_OR_AFTER\"}),\n Plot.dot(reduced_both.sort(function(a, b){return a.BRANCH_LENGTH - b.BRANCH_LENGTH}), {x: \"BRANCH_LENGTH\", y: \"MEAN_PROBABILITY\", fill: \"B4_OR_AFTER\"})\n ],\n color: {\n legend: true\n },\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":516,"value":"md`#### How property affects mean probability for the dataset: ${chosen_dataset}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":469,"value":"Plot.plot({\n marks: [\n Plot.boxY(reduced_both, {x: \"PROPERTY\", y: \"MEAN_PROBABILITY\", fill: \"PROPERTY\"}),\n Plot.dot(reduced_both, {x: \"PROPERTY\", y: \"MEAN_PROBABILITY\", fill: \"B4_OR_AFTER\"})\n ],\n color: {\n legend: true\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":526,"value":"Plot.plot({\n y: {\n grid: true,\n inset: 5\n },\n marks: [\n Plot.boxY(reduced_both, {x: \"NOT_PREDICTED\", y: \"BRANCH_LENGTH\", fill: \"NOT_PREDICTED\"}),\n Plot.dot(reduced_both, {y: \"BRANCH_LENGTH\", x: \"NOT_PREDICTED\", fill: \"B4_OR_AFTER\"}),\n \n ],\n color: {\n legend: true\n },\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":529,"value":"Plot.plot({\n marks: [\n Plot.boxY(reduced_both, {x: \"PROPERTY\", y: \"NOT_PREDICTED\", fill: \"PROPERTY\"}),\n Plot.dot(reduced_both, {x: \"PROPERTY\", y: \"NOT_PREDICTED\", fill: \"B4_OR_AFTER\"})\n ],\n color: {\n legend: true\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":338,"value":"data_and_trees = FileAttachment(\"11-datasets_after_trees@1.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":408,"value":"full_dataset_after = FileAttachment(\"11-datasets_after.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":411,"value":"full_dataset_b4 = FileAttachment(\"11-datasets_b4.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":419,"value":"reduced_after = { \nconst reduced = [];\nfor (let i = 0; i < full_dataset_after.length; i++) {\nif (full_dataset_after[i].DATASET == chosen_dataset){ \n reduced.push(full_dataset_after[i]);\n}\n}\n for (let i = 0; i < reduced.length; i++) {\n reduced[i][\"B4_OR_AFTER\"] = \"AFTER_PRIME_UPDATE\"\n\n}\n return reduced\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":429,"value":"reduced_b4 = { \nconst reduced = [];\nfor (let i = 0; i < full_dataset_b4.length; i++) {\n if (full_dataset_b4[i].DATASET == chosen_dataset){ \n reduced.push(full_dataset_b4[i]);\n}\n}\n for (let i = 0; i < reduced.length; i++) {\n reduced[i][\"B4_OR_AFTER\"] = \"BEFORE_PRIME_UPDATE\"\n\n}\n return reduced\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":455,"value":"reduced_both = {\n const new_list = reduced_b4.concat(reduced_after);\n return new_list\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":320,"value":"tree = new phylotree.phylotree(chosen_tree);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"import {applyHljsStyle} from '@anwarhahjjeffersongeorge/code-block-style-picker'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":281,"value":"import {select, checkbox, autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":313,"value":"d3 = require(\"d3@5\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":316,"value":"phylotree=require ('phylotree@1.0.0-alpha.25')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":331,"value":"stylesheet = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W27","stdlib":"1","titling":"auto"}} 26:"$25:body"