Types of web plugins

The web plugins of Hiplot are divided into three major types.

1. Vue.js front-end + R/other back-end applications (can be called using hctl)
2. Shiny application
3. pure HTML applications

• 1. Volcano, Bubble, Boxplot
• 2. UCSCXenaShiny, Gene ID Convertor, SMART
• 3. sra-explorer, clipboard2markdown, online-encode-decode

Meta JSON

Most of the Hiplot web plugins require Meta JSON for easy retrieval, sorting and querying of meta information for the tools. The demo is shown in the below. Where name, intro, src, href, meta are required fields, which indicate the name of the plugin, a one-sentence introduction, cover image, access path , and other meta information respectively. The file can be used to render the card of web page and right documentation.

Other meta information (meta) includes: score, author, email, issues, citation, releaseDate, updateDate fields, which indicate the rating, author, email, question feedback page, citation information, release date, update date of the tool, respectively.

  {
    "name": {
      "zh_cn": "Sigflow",
      "en": "Sigflow"
    },
    "intro": {
      "zh_cn": "突变 Signature 分析",
      "en": "Mutation Signature Analysis."
    },
    "src": "https://s1.imagehub.cc/images/2020/08/31/3-a6RT9P-tuya.jpg",
    "href": "/advance/sigflow",
    "tag": ["vue", "mutation"],
    "meta": {
      "score": 5,
      "author": "Hiplot Team | Shixiang Wang",
      "email": "wangshx@shanghaitech.edu.cn",
      "issues": "https://github.com/ShixiangWang/sigminer.workflow",
      "citation": "Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis. Shixiang Wang, Ziyu Tao, Tao Wu, Xue-Song Liu. bioRxiv 2020.08.12.247528; doi: https://doi.org/10.1101/2020.08.12.247528",
      "releaseDate": "2020-08-05",
      "updateDate": "2020-08-05"
    }
  }

Rendered front-end：

Data JSON

This file is only needed for developing Vue.js front-end + R/other back-end applications and can be used directly as an input parameter to the hctl command-line application. The demo file is shown below.

# area
{
  "module": "basic",
  "tool": "area",
  "params": {
    "textarea": { "datTable": "" },
    "config": {
      "general": {
        "cmd": "",
        "imageExportType": ["jpeg", "pdf"],
        "size": {
          "width": 4,
          "height": 2.5
        },
        "theme": "theme_bw",
        "palette": "lancet",
        "title": "",
        "alpha": 1
      }
    }
  },
  "exampleData": {
    "config": {
      "general": {
        "title": "Area Plot"
      }
    },
    "textarea": {
      "datTable": "group\txaxis.value\tyaxis.value\nGroup1\t1900\t26\nGroup1\t1901\t27\nGroup1\t1902\t10\nGroup1\t1903\t16\nGroup1\t1904\t19\nGroup1\t1905\t18\nGroup1\t1906\t30\nGroup1\t1907\t27\nGroup1\t1908\t23\nGroup1\t1909\t8\nGroup2\t1900\t10\nGroup2\t1901\t10\nGroup2\t1902\t8\nGroup2\t1903\t6\nGroup2\t1904\t9\nGroup2\t1905\t7\nGroup2\t1906\t10\nGroup2\t1907\t6\nGroup2\t1908\t5\nGroup2\t1909\t3\nGroup3\t1900\t20\nGroup3\t1901\t14\nGroup3\t1902\t14\nGroup3\t1903\t14\nGroup3\t1904\t17\nGroup3\t1905\t17\nGroup3\t1906\t10\nGroup3\t1907\t19\nGroup3\t1908\t11\nGroup3\t1909\t18"
    }
  }
}

Each Data JSON file needs to contain the four fields.

• module (e.g. basic/advance)
• tool (e.g. area/heatmap......)
• params：textarea and config
• exampleData

textarea corresponds to the data tables, and any plugins that requires the use of a data table needs to include the textarea field.

The config stored other core parameters and the general field is required.

• data：Used for data input, holding file and non-table string type data. When the input is a file and exists with the same name as textarea, it can support mode switching between table and file input.
• dataArg：Used to select the specified column of the data table, e.g. Symbol、P.Value、logFc in volcano diagram.
• general：imageExportType sets the export type, size controls the size of the exported image, theme is the ggplot2 theme, palette is the discrete color theme, paletteCont is the continuous color theme, and title is the title name.
• extra：All extra parameters are set in this field.

The textarea, data, dataArg, and extra fields require a UI JSON format file to work.

Heatmap

{
  "module": "basic",
  "tool": "heatmap",
  "params": {
    "textarea": {
      "1-countData": "",
      "2-sampleInfo": "",
      "3-geneInfo": ""
    },
    "config": {
      "data": {
        "1-countData": {
          "value": "",
          "link": ""
        },
        "2-sampleInfo": {
          "value": "",
          "link": ""
        },
        "3-geneInfo": {
          "value": "",
          "link": ""
        }
      },
      "general": {
        "cmd": "",
        "imageExportType": [
          "jpeg",
          "pdf"
        ],
        "size": {
          "width": 8,
          "height": 6
        },
        "title": ""
      },
      "extra": {
        "fontsize_row": 6,
        "fontsize_col": 10,
        "color": "bluered",
        "cluster_rows": true,
        "cluster_cols": true,
        "scale": "none",
        "hc_method": "ward.D2",
        "hc_distance": "euclidean",
        "top_var": 100
      }
    }
  },
  "exampleData": {
    "config": {
      "data": {
        "1-countData": {
          "value": "public/demo/heatmap/countData.txt",
          "link": ""
        },
        "2-sampleInfo": {
          "value": "public/demo/heatmap/sampleInfo.txt",
          "link": ""
        },
        "3-geneInfo": {
          "value": "public/demo/heatmap/geneInfo.txt",
          "link": ""
        }
      },
      "general": {
        "title": "Heatmap Plot"
      }
    },
    "textarea": {
      "1-countData": "Gene\tM1\tM2\tM3\tM4\tM5\tM6\tM7\tM8\tM9\tM10\nGBP4\t6.59934410950219\t5.22626602480198\t3.69328753811098\t3.93850095280092\t4.52719308866722\t9.30811903244735\t8.98786485076655\t7.65831236457275\t8.66603797694234\t7.41970810237923\nBCAT1\t5.7603803773696\t4.89278302092092\t5.4489239172689\t3.48541338578293\t3.85566917175335\t8.66208104047003\t8.79331984841678\t8.76591463653863\t8.09720624308158\t8.26294239938877\nCMPK2\t9.56190511541694\t4.54916815653975\t3.99865492244696\t5.61438398058799\t3.90479287264428\t9.79077000447076\t7.13318755148685\t7.37959101963759\t7.93806251518641\t6.15411790257397\nSTOX2\t8.39640931573611\t8.71705522018908\t8.03906411010794\t7.64305955657731\t9.27464909014892\t4.41701300734515\t4.7252697311358\t3.54221687884127\t4.30518704618541\t6.9647100847245\nPADI2\t8.41976589052513\t8.26842980236139\t8.45118084362689\t9.20073228449025\t8.59820720172578\t4.59003301277654\t5.3682684258907\t4.13666741045992\t4.91098611479878\t4.08036305433613\nSCARNA5\t7.65307430977837\t5.78039262971739\t10.6335504726533\t5.91368436291761\t8.80560475012981\t5.89012047654207\t5.52794464354386\t3.82259606723006\t4.04107769290465\t7.9565886355744\nALOX12P2\t9.00142115218082\t7.75354229108506\t4.92095958179653\t7.63635437094677\t9.88862478901644\t6.21194354380297\t3.73201442207366\t3.70085012794602\t5.37403184307771\t7.80489191906552\nSNORA74B\t5.53870871520511\t7.16905339382908\t11.4416464369403\t5.98256568575252\t8.39440252461064\t4.75155925320549\t5.1812949566099\t4.58719537757651\t5.14743989674245\t7.83076780051947\nHIST1H2BL\t6.18127049664725\t4.44841889018637\t5.60496102984375\t6.48516837385035\t2.59957438666689\t7.63017660565678\t6.7582589826989\t10.1375580321457\t9.0466044917583\t7.13264275153722\nMNDA\t8.70263524951799\t7.32235195639172\t9.27182142017149\t9.13451543974325\t8.33911384365565\t4.57190228487297\t5.47837926919321\t3.92483055805651\t4.63957823676203\t4.63950578262665\nOLFM4\t9.3453083049633\t6.4386066367188\t8.71676126406154\t9.68554516855116\t7.68826184326211\t5.9698038656099\t3.85639196824446\t4.47352687053999\t5.64492097261939\t4.20550714642084\nFLT3\t5.16430632091849\t4.41935544328289\t5.06355136332481\t5.41278353561259\t3.33786341844924\t8.5851643929583\t8.87630237134457\t8.9289219977983\t8.98978132515918\t7.24660387214314\nCHD7\t8.37347496380646\t8.7280322425153\t8.40881760839079\t8.71647551270056\t8.37377066730534\t4.6131990181069\t6.63626044076648\t3.68137997972667\t4.19376832161313\t4.29945528605986\nNFIL3\t8.05541647537976\t8.365099881364\t9.23919367693868\t8.53682507747494\t8.45235081884242\t4.4785271277271\t6.50627030863252\t3.8959926983669\t4.41095238359256\t4.08400559267262\nHSPA1B\t5.0081989999114\t9.19465027714563\t6.59884991799149\t7.12950925125609\t3.88526971724655\t5.71217872524064\t11.1338956120625\t6.39810554739138\t6.46058964785579\t4.50338634489\nAP5B1\t8.23682047357699\t8.97263883679405\t8.20421656900127\t8.43242828422906\t9.22400654256986\t4.42420369458669\t4.86304098388495\t4.2488858417092\t3.85484706645842\t5.56354574818102\nIPCEF1\t8.26306719415969\t9.28785556535855\t8.60223284186519\t8.49115577522355\t8.4476994660962\t4.48393585674786\t5.4599674548191\t3.66895649281438\t4.35921951199522\t4.96054388191175\nLRG1\t8.55308333818146\t9.05332170033288\t9.07450940411854\t8.73670030053071\t7.65633324063663\t4.52994448343282\t5.48766232305694\t4.30479407032271\t3.92420851166188\t4.70407666871694\nTHBS4\t8.88103921226797\t8.8962046751857\t7.84480117149793\t8.73936931675074\t8.62706319627278\t4.69931031212911\t5.28322455941077\t3.22068032857857\t4.73731941895932\t5.09562184993861\nRGL4\t8.45480849703071\t8.01938890687672\t8.99083634468092\t9.71863113099265\t7.90807458680074\t4.14705099091832\t4.98508378739981\t4.57671086951137\t4.93034932889645\t4.2936995978838\nMPP7\t8.69051964227409\t8.63034623763923\t7.08087270300907\t9.8384755216119\t8.27182403778882\t5.17919999372186\t5.20086805964123\t3.26699273882508\t5.56522634026712\t4.30030876621311\nUGCG\t8.64836550117938\t8.60055535380447\t9.43104568751548\t7.9230205615877\t8.3092137937507\t4.90251014386811\t5.75080426564036\t4.49285629867141\t4.65998701082659\t3.30627542414731\nCYSTM1\t8.62888362670211\t9.23867708133921\t8.48724305781585\t8.9585373511481\t7.35710866024406\t4.54160477533\t6.37053294888104\t4.24665066524454\t4.74576899180294\t3.44962688248365\nANXA2\t4.98376888645621\t6.74802153101448\t6.22079149043324\t4.71940343214139\t3.28434591086228\t8.08984980446167\t10.637472034078\t7.21491167389481\t9.00271034808197\t5.12335892956738\nENDOD1\t5.55163971872426\t5.4064649993561\t4.66378474612958\t3.55076540459354\t4.10350671158573\t8.39399071433712\t9.538503098682\t9.06992267005361\t8.63966440241984\t7.10639157510974\nARHGAP24\t6.89007947916903\t8.88394109857622\t9.56065081648397\t8.28567368456581\t9.04375155722334\t3.54400997780181\t4.91918263653937\t4.66479366571633\t4.41046835866553\t5.82208276625007\nCST7\t7.88306127465057\t8.54658456777652\t8.36455313109263\t9.54011011955219\t8.69747335007555\t3.55767433775708\t4.45388730772107\t4.20340520858419\t5.06508165045758\t5.71280309332412\nHIST1H2BM\t6.18690843039134\t4.44880329961322\t5.42877081184887\t6.74768148196589\t2.57757949012244\t7.8282327625163\t6.51781948222203\t10.2068683214703\t9.34519021714569\t6.73677974369545\nEREG\t8.59814505842903\t4.92018356125751\t9.22764453024163\t5.22215712669009\t4.68984964026574\t8.70361683592888\t8.65771352926794\t7.82068826440211\t2.94361803349097\t5.24101746101759\nEMP1\t4.83747543388199\t5.99957641741384\t6.11516842490016\t5.05632301458891\t4.8089296544361\t6.71316401442309\t12.1893065350618\t6.31085309821801\t8.39113699139893\t5.60270045666862\nNFAM1\t8.65629018989617\t9.95728900660463\t7.31990029350576\t8.07351398352073\t9.01665766686702\t4.51762315199373\t4.72270958438004\t3.96195071532599\t4.44051975710331\t5.35817969179413\nSLC40A1\t9.52082184984132\t4.6300860675265\t5.11648649001911\t9.34600283255293\t9.81319155476508\t6.10141574721022\t4.18618228730233\t4.19863910040465\t7.19310786258295\t5.91870024878643\nCD52\t4.23092718292703\t5.93249570901771\t5.01189781226921\t5.10130839611687\t4.3983270843923\t6.3800935538825\t8.98466272397821\t10.2347180028922\t9.80030456111072\t5.94989901440479\nHIST1H2BH\t5.80517708727457\t4.34319698777715\t6.13937959034036\t5.81753025438555\t2.51328424691345\t8.18845818393027\t7.12653567067081\t10.4042857366929\t8.87345797255015\t6.81332831045628\nPFKFB3\t7.42425672770331\t9.67678486447417\t8.93515559526994\t8.04583294946198\t8.89068984047688\t4.27386393159326\t6.23845022648375\t4.09911077395125\t4.18928357412355\t4.2512055574534\nSNORD116-20\t8.37705794265498\t5.35955283281031\t8.69484128728057\t8.044566874355\t2.953568193207\t7.26841856308343\t6.68202099844039\t8.31805239073958\t7.83018011936655\t2.4963748390537\nSTX11\t8.33848786950036\t8.56595435724288\t8.76786820829843\t9.40325703236495\t7.8927019041759\t4.20583487558089\t6.56566629172552\t3.93102359732804\t5.05044318547588\t3.30339671929864\nSYNE2\t9.11072611328461\t9.67836134625684\t8.40561173679154\t6.94624220725133\t8.15607283894003\t5.79100701147425\t6.83726740779878\t3.72229368939695\t3.64064574323032\t3.73640594656685\nTCN1\t8.19317939308718\t8.90728488343263\t8.71384756012029\t8.98092755959508\t7.62755788426105\t4.62660939758871\t7.35405470412209\t3.26529168007395\t5.10839832356915\t3.24748265514137\nSNORA74A\t5.4989036434177\t5.06210341418121\t12.5614991243383\t5.83920176184402\t7.58105067734548\t5.49829568381575\t5.02357896739217\t5.50173428262313\t5.4573021976407\t8.00096428839304\nCD74\t5.01744308932942\t5.38397759336954\t3.40565075861287\t3.26432655177697\t5.60296552976606\t8.55015684287963\t8.4645233512142\t8.13241016875959\t8.5163423184491\t9.68683783683414\nEIF4E3\t9.36688761928368\t8.36018887001937\t5.65505213371847\t4.28772104579371\t8.71376536348066\t8.88080109689556\t6.41739276540472\t3.40585799587955\t3.25180217037193\t7.68516498014385\nMYO7B\t8.79611534432829\t9.26583690983665\t7.8656404761721\t8.78531999135262\t9.20970307578869\t4.27220206662578\t4.86618816582842\t4.31029972560557\t3.75857526199639\t4.89475302345698\nMX1\t10.7399030893231\t4.50404260897076\t4.71430259549509\t6.24479780351586\t4.89150097148067\t10.7278791187166\t5.65352833761679\t5.43046577412365\t7.73404493141918\t5.38416881032981\nLDLR\t3.3023953681893\t10.5824300145645\t6.20991327444613\t3.80421415609279\t4.63139094647011\t5.53404635380304\t9.43371508056491\t7.63273933233868\t7.48857857686732\t7.40521093765471\nS100P\t8.35636294936595\t7.91549084154158\t9.48176980003573\t9.64299277807315\t8.36351939921641\t3.69945055381311\t5.68894296460362\t4.35319019179119\t4.53125428970718\t3.99166027284357\nPTPRCAP\t5.02866699715586\t4.72401054711007\t4.12222935711548\t4.18894761345505\t3.80305085836535\t8.52515867110778\t9.16970132164356\t8.84671238588808\t9.08012596508563\t8.53603032406465\nKIT\t5.88821169660724\t2.53319368811524\t5.07711091817713\t4.744692934599\t4.83905051253733\t9.085158267425\t6.46904009029344\t8.93318564462529\t9.05670746922666\t9.39828281938518\nOLR1\t9.01868187619349\t7.93695732170955\t9.39089698487919\t8.89799447847056\t8.66892458672748\t5.26159497530433\t5.04252044319123\t3.57871573392495\t4.84845427537843\t3.3798933652123\nNKG7\t7.31252298211301\t10.372963701899\t7.93774381957631\t8.16124853471517\t9.67105074612135\t4.16407599495347\t4.99276125377779\t4.20468881354564\t3.82412866616305\t5.3834495281267\n",
      "2-sampleInfo": "Sample\tGroup\tAge\nM1\tControl\t23\nM2\tControl\t34\nM3\tControl\t25\nM4\tControl\t52\nM5\tControl\t36\nM6\tCancer\t28\nM7\tCancer\t31\nM8\tCancer\t22\nM9\tCancer\t29\nM10\tCancer\t34",
      "3-geneInfo": "Gene\tPathway\nGBP4\tCancer\nBCAT1\tCancer\nCMPK2\tCancer\nSTOX2\tCancer\nPADI2\tCancer\nSCARNA5\tCancer\nALOX12P2\tCancer\nSNORA74B\tCancer\nHIST1H2BL\tCancer\nMNDA\tCancer\nOLFM4\tCancer\nFLT3\tCancer\nCHD7\tCancer\nNFIL3\tCancer\nHSPA1B\tCancer\nAP5B1\tCancer\nIPCEF1\tCancer\nLRG1\tCancer\nTHBS4\tCancer\nRGL4\tCancer\nMPP7\tCancer\nUGCG\tMetabolism\nCYSTM1\tMetabolism\nANXA2\tMetabolism\nENDOD1\tMetabolism\nARHGAP24\tMetabolism\nCST7\tMetabolism\nHIST1H2BM\tMetabolism\nEREG\tMetabolism\nEMP1\tMetabolism\nNFAM1\tMetabolism\nSLC40A1\tMetabolism\nCD52\tMetabolism\nHIST1H2BH\tMetabolism\nPFKFB3\tMetabolism\nSNORD116-20\tMetabolism\nSTX11\tMetabolism\nSYNE2\tMetabolism\nTCN1\tMetabolism\nSNORA74A\tMetabolism\nCD74\tMetabolism\nEIF4E3\tMetabolism\nMYO7B\tMetabolism\nMX1\tMetabolism\nLDLR\tMetabolism\nS100P\tMetabolism\nPTPRCAP\tMetabolism\nKIT\tMetabolism\nOLR1\tMetabolism\nNKG7\tMetabolism"
    }
  }
}

Volcano

{
  "module": "basic",
  "tool": "volcano",
  "params": {
    "textarea": {
      "datTable": ""
    },
    "config": {
      "dataArg": {
        "datTable": [
          {
            "value": ""
          },
          {
            "value": ""
          },
          {
            "value": ""
          }
        ]
      },
      "general": {
        "cmd": "",
        "imageExportType": [
          "jpeg",
          "pdf"
        ],
        "size": {
          "width": 4.5,
          "height": 3
        },
        "theme": "theme_bw",
        "palette": "lancet",
        "title": "",
        "alpha": 0.5
      },
      "extra": {
        "p_cutoff": 0.05,
        "fc_cutoff": 2,
        "show_top": true,
        "show_genes_num": 10,
        "selected_genes": []
      }
    }
  },
  "exampleData": {
    "config": {
      "dataArg": {
        "datTable": [
          {
            "value": "Symbol"
          },
          {
            "value": "P.Value"
          },
          {
            "value": "logFC"
          }
        ]
      },
      "general": {
        "title": "Volcano Plot"
      }
    },
    "textarea": {
      "datTable": "Symbol\tlogFC\tP.Value\nLTB\t2.580830574\t1.17E-14\nCDCA5\t-2.326302376\t2.46E-13\nC10orf54\t3.307901298\t3.53E-13\nCAPN7\t2.514235402\t1.04E-12\nOIP5\t-2.16662036\t1.43E-12\nSNORD116-2\t3.139661776\t2.15E-12\nPKIG\t-1.560503944\t1.58E-12\nEMCN\t3.681695861\t2.68E-12\nB2M\t1.578095238\t2.82E-12\nIL6ST\t2.287862908\t5.51E-12\nSNORD90\t4.285534102\t6.12E-12\nDUSP6\t3.01388868\t7.90E-12\nRBMS1\t2.251183421\t8.82E-12\nC4orf18\t4.252879583\t1.17E-11\nSKAP1\t3.112284552\t1.80E-11\nCD48\t1.8697202\t1.89E-11\nF11R\t2.647752591\t1.99E-11\nZNF83\t2.854695072\t2.93E-11\nKIAA0664\t-1.565376538\t3.34E-11\nSETBP1\t2.23996263\t3.90E-11\nTNFSF10\t3.044122513\t3.87E-11\nSMOX\t2.191591775\t4.85E-11\nFAIM3\t3.789600438\t4.90E-11\nNLRP1\t1.637345982\t6.18E-11\nSNORD11B\t2.731552213\t5.99E-11\nSHCBP1\t-1.764536246\t7.34E-11\nTUBA4A\t2.699864676\t7.56E-11\nSNORD45A\t3.17650067\t9.76E-11\nGAS2\t1.794776006\t1.05E-10\nDENND4C\t2.532413268\t1.16E-10\nCENTD1\t3.840179499\t1.23E-10\nSTX16\t1.753540316\t1.41E-10\nGLTP\t2.466056912\t1.41E-10\nSUCLG2\t2.928543297\t1.57E-10\nNCAPD3\t-1.781520666\t1.67E-10\nFBXO30\t2.632198292\t1.78E-10\nMCTP1\t2.494353116\t1.96E-10\nTMEM106B\t2.641348607\t2.18E-10\nANXA4\t2.589776199\t2.26E-10\nBRI3\t2.32304862\t2.65E-10\nSCMH1\t2.534410245\t2.81E-10\nEFNA1\t2.061209663\t3.17E-10\nLOC100216545\t2.563903745\t3.23E-10\nTFPI\t2.768874139\t3.47E-10\nDOCK10\t1.574819826\t3.58E-10\nPLEC1\t2.046811325\t4.21E-10\nNBPF14\t1.631133914\t4.26E-10\nGNAI1\t3.292962351\t4.50E-10\nDNAJB14\t1.762813394\t4.64E-10\nSPIN1\t1.89821937\t4.90E-10\nC3orf65\t2.486153394\t5.10E-10\nSNORA40\t3.032186515\t5.13E-10\nJAK3\t1.673176313\t5.36E-10\nDAPP1\t2.773503453\t5.53E-10\nCIDECP\t1.673952095\t5.52E-10\nBAT1\t1.659285974\t6.52E-10\nCD302\t3.143917019\t6.41E-10\nHIST2H2BF\t2.107694721\t7.38E-10\nTSC22D3\t1.348915568\t7.35E-10\nJMY\t2.973822067\t7.99E-10\nWDR4\t-1.310110292\t8.66E-10\nWFS1\t3.231184469\t9.04E-10\nPPP1R15B\t2.941824385\t9.31E-10\nTNFRSF10D\t2.420104255\t9.79E-10\nSNORD101\t3.125526526\t9.89E-10\nWBP5\t2.732004269\t9.91E-10\nCCBL2\t3.112615008\t1.01E-09\nPDCD2L\t-2.113055026\t1.04E-09\nSLK\t2.884328183\t1.04E-09\nCAPN2\t2.124368974\t1.13E-09\nC1orf27\t2.935836151\t1.25E-09\nLOC54103\t2.739359464\t1.42E-09\nGIMAP8\t2.956962963\t1.43E-09\nDYNLT3\t2.723945192\t1.50E-09\nCD320\t-0.974251062\t1.58E-09\nC7orf43\t1.810778464\t1.65E-09\nTMEM38B\t3.008491233\t1.64E-09\nSNRK\t1.865929972\t1.86E-09\nSNRK\t1.891882225\t1.89E-09\nPHYH\t2.121411408\t1.99E-09\nSNX10\t3.18236194\t2.00E-09\nPPP2CB\t3.317414573\t2.22E-09\nEID3\t2.498561617\t2.23E-09\nLOC153561\t1.669940216\t2.34E-09\nVEZT\t3.154359576\t2.31E-09\nPREX2\t2.624955415\t2.32E-09\nCD74\t2.264093985\t2.33E-09\nHIST2H2BE\t2.822447195\t2.50E-09\nSEL1L3\t1.452464322\t2.53E-09\nNAP1L1\t2.525931404\t2.73E-09\nPTTG3P\t-1.2886861\t2.74E-09\nGNA13\t2.984842773\t2.79E-09\nALDH1A1\t2.805007303\t2.82E-09\nRFWD2\t1.320951986\t2.98E-09\nRNF149\t2.001710859\t2.99E-09\nMN1\t1.650245511\t3.06E-09\nUBE2T\t-2.642575162\t3.08E-09\nGBP2\t1.849700828\t3.30E-09\nUHRF1\t-1.498478196\t3.32E-09\nDDX17\t1.355291128\t3.43E-09\nDVL2\t1.567126145\t3.45E-09\nC8orf33\t1.61634479\t3.52E-09\nKCTD6\t2.741615683\t3.54E-09\nREL\t2.616629244\t3.76E-09\nPLEKHA5\t2.157890626\t3.75E-09\nPDXDC2\t2.412685822\t3.84E-09\nCYP51A1\t2.269862597\t3.94E-09\nC6orf204\t2.650498256\t3.94E-09\nPPM1D\t1.838008448\t4.02E-09\nC1orf52\t2.209529981\t4.12E-09\nPFDN5\t1.184332\t4.11E-09\nSNORD15A\t3.106151098\t4.47E-09\nC11orf71\t2.213827794\t4.45E-09\nSLC5A10\t3.32741743\t4.73E-09\nSNORD58A\t2.633392176\t4.73E-09\nKIF16B\t2.899153367\t4.83E-09\nC20orf106\t2.45895529\t4.85E-09\nFBXO11\t2.968344081\t5.21E-09\nG3BP2\t2.438734867\t5.23E-09\nTUBB4Q\t1.755223987\t5.41E-09\nAES\t2.650892668\t5.43E-09\nPYGL\t1.530968225\t5.55E-09\nSNORD57\t2.174552314\t5.56E-09\nNR4A2\t2.615482307\t5.76E-09\nCENPH\t-2.19106195\t5.81E-09\nBMP6\t2.636175343\t6.09E-09\nECE2\t-3.098961372\t6.32E-09\nSLC30A3\t2.392841012\t6.71E-09\nMYCT1\t2.728250017\t6.73E-09\nDUSP11\t1.874551148\t7.50E-09\nHLA-C\t3.623823362\t7.50E-09\nPTGS2\t3.325491831\t7.72E-09\nNPIP\t1.2141338\t7.94E-09\nNMD3\t2.556687502\t8.20E-09\nNHLRC3\t2.188286202\t8.41E-09\nTP53INP1\t1.694127564\t8.74E-09\nHLA-DMB\t0.918279148\t9.00E-09\n43166\t2.927183144\t9.26E-09\nEFHC2\t1.989834569\t9.32E-09\nHECA\t2.57491547\t9.71E-09\nACSF2\t2.784113269\t9.73E-09\nITGAX\t2.380372559\t1.00E-08\nSNORD109A\t2.568549382\t1.01E-08\nCDCA4\t-2.582205642\t1.03E-08\nSeptin 2\t2.42105794\t1.04E-08\nGABBR1\t2.564331292\t1.07E-08\nTAPBP\t1.704721108\t1.08E-08\nKPNA6\t1.129223094\t1.14E-08\nATP5G1\t-1.244276948\t1.15E-08\nLOC728855\t2.939539196\t1.19E-08\nZNF655\t2.146976359\t1.19E-08\nGIMAP2\t2.616881069\t1.26E-08\nSNORD54\t3.049868661\t1.27E-08\nWDR33\t1.948287195\t1.34E-08\nPREX2\t3.285895384\t1.35E-08\nSCFD1\t2.600587841\t1.40E-08\nCRYM\t-3.238068573\t1.41E-08\nNDUFA12\t-0.848197348\t1.45E-08\nADIPOR1\t2.851473731\t1.48E-08\nRAPGEF3\t2.693761519\t1.58E-08\nASGR1\t2.290184317\t1.60E-08\nAMMECR1L\t1.711783887\t1.75E-08\nARHGAP27\t1.770732045\t1.76E-08\nATG16L1\t-1.568648562\t1.78E-08\nARGLU1\t1.682967662\t1.79E-08\nTTC14\t2.681213309\t1.81E-08\nPIK3C2A\t2.600816364\t1.81E-08\nFAM108B1\t2.166117703\t1.89E-08\nETS1\t2.777475458\t1.89E-08\nLIN7C\t2.069317387\t1.95E-08\nMAN1A1\t2.467221656\t1.97E-08\nTMEM70\t1.459796049\t2.01E-08\nSCARNA1\t2.665515293\t2.01E-08\n7A5\t2.376298384\t2.07E-08\nSNORA53\t2.401449051\t2.09E-08\nSNORA11\t2.322649296\t2.14E-08\nKIAA1191\t1.915860872\t2.15E-08\nKCNK5\t-2.518390469\t2.30E-08\nRPS21\t-1.170227058\t2.32E-08\nTERF1\t1.638389068\t2.37E-08\nWSB1\t1.069996842\t2.37E-08\nGATAD1\t1.679118217\t2.43E-08\nNR4A3\t2.137548814\t2.45E-08\nGOLGA6\t1.763912508\t2.51E-08\nERG\t2.972707379\t2.52E-08\nMALT1\t2.26037905\t2.55E-08\nHERPUD2\t1.900667585\t2.56E-08\nLCOR\t2.863017349\t2.68E-08\nARL4A\t2.534282385\t2.68E-08\nIQCA1\t1.799161113\t2.76E-08\nTM2D1\t2.591118647\t2.78E-08\nUCK2\t-1.089567526\t2.88E-08\nSMURF1\t2.213575609\t2.92E-08\nSP1\t2.296459764\t2.99E-08\nTADA1L\t1.926722058\t3.01E-08\nSNORD60\t2.401728236\t3.10E-08\nP2RY5\t2.204663192\t3.13E-08\nRRP1B\t2.085705853\t3.24E-08\nNR4A2\t3.358040068\t3.24E-08\nC12orf31\t2.434593945\t3.38E-08\nTMED7\t2.64503761\t3.41E-08\nPNRC2\t1.969004393\t3.44E-08\nFAM164A\t1.843772505\t3.51E-08\nGART\t-1.351433354\t3.61E-08\nUBR7\t-1.435194528\t3.62E-08\nSTARD4\t2.224089317\t3.83E-08\nKIAA0101\t-2.920414589\t3.84E-08\nPLAGL1\t1.853212055\t3.97E-08\nIGLL1\t-2.297869085\t4.02E-08\nSPAG9\t2.233964196\t4.11E-08\nACE\t1.496120153\t4.14E-08\nPTPN22\t2.444700116\t4.28E-08\nCLK1\t2.526763799\t4.33E-08\nNOP14\t2.261392002\t4.40E-08\nALDH6A1\t1.762876928\t4.42E-08\nFAM98A\t1.571431616\t4.50E-08\nADD3\t2.584354917\t4.51E-08\nC1orf85\t1.451055504\t4.66E-08\nPEAR1\t2.32583453\t4.69E-08\nCRLF3\t2.143178781\t4.79E-08\nAGL\t2.390643324\t4.85E-08\nC2orf32\t-4.393018768\t4.97E-08\nTSC22D2\t2.893539092\t4.99E-08\nKIAA1143\t2.386606962\t5.20E-08\nFAM120AOS\t1.833994649\t5.23E-08\nARL4A\t2.628451682\t5.52E-08\nEHD2\t2.507711389\t5.51E-08\nTCEAL3\t2.592378097\t5.64E-08\nACBD3\t2.202158272\t5.74E-08\nSLC25A19\t-1.786317456\t5.84E-08\nLRP1\t2.439869094\t5.85E-08\nMARCKS\t1.57127199\t5.95E-08\nFUT11\t2.140072864\t6.04E-08\nFBXO3\t1.699236697\t6.06E-08\nZNF644\t2.21248374\t6.12E-08\nWBP2\t1.07050078\t6.29E-08\nKIF27\t2.673535202\t6.32E-08\nPKMYT1\t-4.42290933\t6.46E-08\nAMD1\t2.599648671\t6.48E-08\nRNF103\t2.327445671\t6.60E-08\nSKP1\t2.011967001\t6.59E-08\nGRK5\t1.804758477\t6.79E-08\nRPS23\t1.484142372\t6.83E-08\nMETTL9\t1.859259752\t6.94E-08\nHOXA2\t2.126448566\t6.93E-08\nDCBLD2\t3.336851659\t7.09E-08\nMTFMT\t1.998551051\t7.13E-08\nCENPN\t-0.861824614\t7.21E-08\nST13\t1.231982764\t7.21E-08\nLOC440354\t1.628840962\t7.26E-08\nIFNAR2\t1.890839122\t7.36E-08\nSNORA21\t1.87845627\t7.63E-08\nCARD16\t2.811988831\t7.71E-08\nCXorf21\t2.526566943\t7.81E-08\nKIAA0240\t1.660318907\t7.88E-08\nAIF1\t1.649946816\t7.98E-08\nOAS3\t1.407428078\t8.00E-08\nRNF13\t1.878881286\t8.10E-08\nZNF514\t1.605437562\t8.17E-08\nTCEAL1\t2.366326534\t8.37E-08\nHOXA9\t2.269711736\t8.43E-08\nSPON2\t-1.990975545\t8.59E-08\nSELK\t2.416620159\t8.59E-08\nTHUMPD1\t1.91383205\t8.85E-08\nSDAD1\t1.127485936\t8.87E-08\nDKFZP564O0523\t2.586508268\t8.96E-08\nASXL2\t2.491785167\t8.99E-08\nATP6V1C1\t2.343858942\t9.19E-08\nC1orf43\t2.099332016\t9.24E-08\nCD44\t1.342161754\t9.46E-08\nPTPRE\t1.73773728\t9.50E-08\nSNORD76\t2.570643097\t9.62E-08\nSNORD114-3\t2.591413172\t9.77E-08\nZMAT1\t2.348465353\t9.87E-08\nUBE3C\t1.873475224\t9.87E-08\nC7orf23\t1.55543335\t1.00E-07\nKIAA1600\t2.47904252\t1.00E-07\nIQGAP2\t2.293080363\t1.03E-07\nCOPS8\t2.503755753\t1.03E-07\nSFRS5\t1.971978562\t1.05E-07\nBARD1\t-1.138523468\t1.05E-07\nMKI67IP\t1.846953972\t1.07E-07\nZNF141\t2.064901931\t1.08E-07\nP4HA1\t1.829654049\t1.09E-07\nNCOR2\t1.845832019\t1.10E-07\nCFI\t2.365700077\t1.15E-07\nSEC24B\t1.928552221\t1.15E-07\nPOGZ\t1.506056234\t1.17E-07\nPPIL5\t2.235695033\t1.17E-07\nAHR\t1.432813094\t1.21E-07\nCLEC3B\t2.456871624\t1.23E-07\nDNAJB14\t1.831608383\t1.26E-07\nCCNG1\t2.6483916\t1.26E-07\nGCC1\t2.154361434\t1.28E-07\nFAM91A1\t2.113188908\t1.28E-07\nC10orf84\t-2.455492056\t1.30E-07\nCYSLTR1\t2.724640669\t1.30E-07\nHEMGN\t2.176900188\t1.32E-07\nSRP14\t2.411026421\t1.32E-07\nVPS24\t2.946390908\t1.36E-07\nSOCS2\t1.31095286\t1.36E-07\nSMAD5\t2.169176715\t1.36E-07\nCCNE1\t-1.42558521\t1.37E-07\nTECR\t-1.110361996\t1.39E-07\nPSMA2\t2.705394625\t1.40E-07\nUSP16\t1.976526816\t1.45E-07\nSNX16\t2.609985369\t1.45E-07\nC7orf46\t1.73332848\t1.50E-07\nLEF1\t-3.069406149\t1.50E-07\nST3GAL5\t1.513777076\t1.52E-07\nPRKACB\t2.048330831\t1.53E-07\nTSEN15\t2.19346509\t1.54E-07\nVAPA\t1.861531303\t1.55E-07\nALDH5A1\t2.277101162\t1.56E-07\nGSTA4\t2.226007559\t1.56E-07\nCES8\t2.267740546\t1.60E-07\nRABGEF1\t2.203167433\t1.60E-07\nSLC16A3\t2.375538102\t1.62E-07\nNIPBL\t2.744032293\t1.63E-07\nPKN2\t1.942238174\t1.68E-07\nSKA2\t2.023151069\t1.68E-07\nSNORD11\t2.701904409\t1.71E-07\nKCNK17\t2.068072071\t1.72E-07\nZNF281\t2.051549636\t1.74E-07\nCEP57\t1.915860604\t1.76E-07\nABT1\t1.720885211\t1.79E-07\nASH1L\t2.415843421\t1.80E-07\nLOC100190986\t1.073391958\t1.82E-07\nCDC16\t2.238114418\t1.85E-07\nFBXW11\t2.214988414\t1.87E-07\nC6orf173\t-0.943950518\t1.88E-07\nPRKACB\t2.61301041\t1.89E-07\nSNORA2A\t1.847064421\t1.90E-07\nETV3\t1.519548507\t1.93E-07\nCDC14A\t2.415482757\t1.93E-07\nHNRPK\t2.341759444\t1.95E-07\nGPD2\t1.778375115\t1.96E-07\nMST4\t2.104496278\t1.99E-07\nDDX59\t2.162610575\t2.01E-07\nNBEA\t2.249510396\t2.03E-07\nRORA\t2.77182728\t2.03E-07\nSTEAP3\t-2.372817165\t2.06E-07\nMTMR2\t2.295993977\t2.06E-07\nMGC21881\t1.375595708\t2.09E-07\nSEC62\t1.756600314\t2.10E-07\nZMYM5\t1.715306173\t2.14E-07\nHIST1H2BD\t2.909347531\t2.15E-07\nPPM2C\t1.996730593\t2.21E-07\nPLEKHA1\t1.769819129\t2.23E-07\nRNF19B\t1.844216651\t2.27E-07\nTBC1D9B\t1.97326931\t2.27E-07\nOFD1\t1.81652763\t2.28E-07\nPPP4R1\t2.039613541\t2.32E-07\nVPS36\t1.42957004\t2.33E-07\nTROVE2\t2.848900373\t2.38E-07\nSPI1\t2.192249768\t2.40E-07\nKCNH2\t-3.827473531\t2.40E-07\nTRAF6\t2.150451786\t2.48E-07\nSEC24A\t1.717888212\t2.52E-07\nTIAF1\t2.39618237\t2.59E-07\nTINP1\t2.051366765\t2.60E-07\nTNFRSF10B\t1.428222834\t2.63E-07\nUBE2N\t2.703990892\t2.63E-07\nITPKA\t-1.958926857\t2.64E-07\nMTPN\t2.326510264\t2.65E-07\nCDC37L1\t2.374142546\t2.70E-07\nIDI1\t2.213495663\t2.73E-07\nRNF8\t2.227849247\t2.83E-07\nHNRPH1\t2.246772599\t2.83E-07\nBFAR\t1.877853113\t2.85E-07\nNCK2\t1.776392793\t2.87E-07\nLRRC8C\t2.691372552\t2.92E-07\nARL4A\t2.479737733\t2.94E-07\nCD79B\t0.949290638\t2.98E-07\nSKA2\t1.320172448\t2.99E-07\nSNORD33\t1.011008212\t3.02E-07\nFAM119A\t2.1674084\t3.02E-07\nUSP44\t2.652099182\t3.05E-07\nZNF233\t2.364625244\t3.06E-07\nSNORD4A\t1.550448639\t3.11E-07\nRRAS2\t1.963799455\t3.12E-07\nIFNGR2\t0.783760138\t3.13E-07\nZNF321\t2.330586449\t3.14E-07\nKIAA0090\t1.66416609\t3.17E-07\nSNORA14A\t2.241641744\t3.19E-07\nHTATIP2\t2.166712034\t3.26E-07\nDYNLRB1\t2.092006552\t3.26E-07\nC9orf36\t1.833880107\t3.31E-07\nARID2\t2.340857852\t3.33E-07\nDSE\t2.016522156\t3.37E-07\nZNF322A\t2.551239821\t3.39E-07\nSFRS10\t2.262171784\t3.42E-07\nCALM1\t2.240151135\t3.43E-07\nPHLDB1\t2.35772501\t3.45E-07\nZNF189\t2.309132877\t3.46E-07\nNLRX1\t1.54439703\t3.57E-07\nFAM107B\t1.750561694\t3.57E-07\nMYST4\t2.319392767\t3.64E-07\nSPOP\t1.705052805\t3.64E-07\nCGRRF1\t1.551013591\t3.69E-07\nC2orf49\t2.350654597\t3.69E-07\nPPP2CA\t2.480923474\t3.70E-07\nSFRS11\t2.554549316\t3.73E-07\nC17orf63\t1.49330862\t3.77E-07\nPGRMC2\t2.304943821\t3.77E-07\nTUBG1\t-1.54953068\t3.81E-07\nTOPORS\t1.31862355\t3.81E-07\nSPAST\t1.602222208\t3.91E-07\nSNORD77\t1.410571838\t3.92E-07\nING3\t2.235265329\t3.96E-07\nTNFRSF10A\t1.910839237\t3.97E-07\nMYO18A\t1.961139837\t4.06E-07\nTFB2M\t1.574348636\t4.07E-07\nRBBP6\t1.849247439\t4.13E-07\nTP53INP1\t1.63476274\t4.15E-07\nSNORD95\t1.362838182\t4.16E-07\nKIAA1267\t0.69770044\t4.20E-07\nFRMPD2\t-4.26738285\t4.27E-07\nSNX7\t1.904087625\t4.27E-07\nC1D\t2.365042737\t4.42E-07\nSNORD30\t1.054145772\t4.43E-07\nSP110\t1.290589624\t4.47E-07\nNUMB\t2.022085553\t4.47E-07\nGNAI3\t1.935612448\t4.52E-07\nCD83\t1.879895841\t4.53E-07\nPHKB\t-1.338589404\t4.61E-07\nAGTPBP1\t1.726221136\t4.63E-07\nDYRK3\t2.38217318\t4.65E-07\nMRPL47\t2.052328952\t4.71E-07\nCOQ10B\t1.49671389\t4.81E-07\nTCEAL1\t2.313689413\t4.82E-07\nCSTF2T\t2.656762233\t4.93E-07\nTSPYL2\t2.012978847\t4.94E-07"
    }
  }
}

UI JSON

The UI JSON file is mainly used to automatically render the Vue.js application front-end. It consists of three fields.

• data
• dataArg
• extra

General parameters can be configured automatically based on the presence or absence of fields, so there is no need to configure them in the UI JSON, the minimal example format is as follows.

{
  "data": {
    "datTable": {
      "type": "hiplot-textarea",
      "required": true,
      "label": {
        "zh_cn": "数据表",
        "en": "Data Table"
      },
    }
  }
}

data supported types：

• hiplot-textarea: Spreadsheet-based table.
• cloud-file File selection.
• combobox Text input.
• codemirror Input codes.

extra supportted types：

• slider
• switch
• select
• autocomplete
• combobox
• color-picker
• text-field

All fields and types can be extended, refer to：https://vuetifyjs.com/en/components/autocompletes.

items_func: The select box can be optionally parameterized by executing a JavaScript function, where the this.selectCols function can be used to get all the values of a column as selectable items based on the front-end data table (the first parameter is the data table field name, the second parameter specifies the column, counting from 0).

if set UI components to be displayed via check the one of the extra field.

if_func can set whether the UI is displayed or not by executing JavaScript functions. You can get the value in the Data JSON by using this.params.

class can set the class of the component, where col, col-xs, col-md, col-lg, col-xl + the number (1-12) can responsively control the element width. Detailed reference：https://vuetifyjs.com/en/features/breakpoints/#usage。

Heatmap

{
  "data": {
    "1-countData": {
      "type": "hiplot-textarea",
      "required": true,
      "label": "messages.basic.heatmap.countData"
    },
    "2-sampleInfo": {
      "type": "hiplot-textarea",
      "required": false,
      "label": {
        "en": "SampleInfo",
        "zh_cn": "样本信息"
      }
    },
    "3-geneInfo": {
      "type": "hiplot-textarea",
      "required": false,
      "label": {
        "en": "GeneInfo",
        "zh_cn": "基因信息"
      }
    }
  },
  "extra": {
    "color": {
      "type": "select",
      "label": "messages.basic.heatmap.color",
      "items": [
        "bluered",
        "greenred",
        "heat",
        "methylation"
      ],
      "class": "col-12 col-md-6"
    },
    "scale": {
      "type": "select",
      "label": "messages.basic.common.scale",
      "items": [
        "none",
        "row",
        "column"
      ],
      "class": "col-12 col-md-6"
    },
    "hc_method": {
      "type": "select",
      "label": "messages.basic.common.hc_method",
      "items": [
        "ward.D",
        "ward.D2",
        "single",
        "complete",
        "average",
        "mcquitty",
        "median",
        "centroid"
      ],
      "class": "col-12 col-md-6"
    },
    "hc_distance": {
      "type": "select",
      "label": "messages.basic.common.hc_distance",
      "items": [
        "euclidean",
        "maximum",
        "manhattan",
        "canberra",
        "binary",
        "minkowski"
      ],
      "class": "col-12 col-md-6"
    },
    "fontsize_row": {
      "type": "slider",
      "label": "messages.basic.common.fontsizeRow",
      "class": "col-12 col-md-6"
    },
    "fontsize_col": {
      "type": "slider",
      "label": "messages.basic.common.fontsizeCol",
      "class": "col-12 col-md-6"
    },
    "cluster_rows": {
      "type": "switch",
      "label": "messages.basic.common.cluster_rows",
      "class": "col-12 col-md-4"
    },
    "cluster_cols": {
      "type": "switch",
      "label": "messages.basic.common.cluster_cols",
      "class": "col-12 col-md-4"
    },
    "top_var": {
      "type": "slider",
      "label": {
        "zh_cn": "Top 方差",
        "en": "Top Variance"
      },
      "min": 1,
      "class": "col-12"
    }
  }
}

Volcano

{
  "data": {
    "datTable": {
      "type": "hiplot-textarea",
      "required": true,
      "label": "messages.common.dataTable"
    }
  },
  "dataArg": {
    "datTable": [
      {
        "label": "Symbol"
      },
      {
        "label": "P.Value"
      },
      {
        "label": "logFC"
      }
    ]
  },
  "extra": {
    "p_cutoff": {
      "type": "slider",
      "label": "messages.basic.volcano.pCutoff",
      "min": 0,
      "max": 1,
      "step": 0.001,
      "class": "col-12 col-md-6"
    },
    "fc_cutoff": {
      "type": "slider",
      "label": "messages.basic.volcano.fcCutoff",
      "step": 0.1,
      "class": "col-12 col-md-6"
    },
    "show_top": {
      "type": "switch",
      "label": "messages.basic.volcano.showTop",
      "class": "col-12"
    },
    "show_genes_num": {
      "type": "slider",
      "label": "messages.basic.volcano.show_genes_num",
      "class": "col-12 col-md-6",
      "if": "show_top",
      "max": 500
    },
    "selected_genes": {
      "type": "autocomplete",
      "multiple": true,
      "label": "messages.basic.volcano.selected_genes",
      "class": "col-12 col-md-6",
      "if": "show_top",
      "items_func": "this.selectCols('datTable', 0)"
    }
  }
}

Bubble

{
  "data": {
    "datTable": {
      "type": "hiplot-textarea",
      "required": true,
      "label": "messages.common.dataTable"
    }
  },
  "dataArg": {
    "datTable": [
      {
        "label": "Term"
      },
      {
        "label": "Count"
      },
      {
        "label": "Ratio"
      },
      {
        "label": "P.value"
      }
    ]
  },
  "extra": {
    "topnum": {
      "type": "slider",
      "label": "messages.basic.bubble.topnum",
      "max": 300,
      "class": "col-12 col-md-6"
    },
    "pq_value": {
      "type": "select",
      "label": "messages.basic.bubble.pq_value",
      "class": "col-12 col-md-6",
      "items": ["Q Value", "P Value", "FDR"]
    },
    "low_color": {
      "type": "color-picker",
      "label": "messages.basic.common.low_color",
      "class": "col-12 col-md-4"
    },
    "high_color": {
      "type": "color-picker",
      "label": "messages.basic.common.high_color",
      "class": "col-12 col-md-4"
    }
  }
}

GISTIC2

{
  "data": {
    "input": {
      "type": "cloud-file",
      "required": true,
      "label": {
        "zh_cn": "Segmentation 文件",
        "en": "Segmentation File"
      },
      "icon": "mdi-file",
      "exts": [
        "txt"
      ],
      "enable-download": true,
      "enable-preview": true,
      "enable-upload": true
    }
  },
  "extra": {
    "refgenefile": {
      "type": "select",
      "label": {
        "en": "Reference Genome Version",
        "zh_cn": "参考基因版本"
      },
      "items": [
        "hg16.mat",
        "hg17.mat",
        "hg18.mat",
        "hg19.mat",
        "hg19.UCSC.add_miR.140312.refgene.mat",
        "hg38.UCSC.add_miR.160920.refgene.mat"
      ],
      "class": "col-12"
    },
    "brlen": {
      "type": "slider",
      "label": {
        "en": "Threshold (broad form focal events)",
        "zh_cn": "阈值 (broad form focal events)"
      },
      "min": 0,
      "max": 1,
      "step": 0.01,
      "class": "col-12"
    },
    "maxseg": {
      "type": "slider",
      "label": {
        "en": "Maximum number of segments (K)",
        "zh_cn": "片段最大值 (K)"
      },
      "min": 0,
      "max": 100,
      "step": 0.01,
      "class": "col-12"
    },
    "confidence": {
      "type": "slider",
      "label": {
        "en": "Confidence Level of Region Driver",
        "zh_cn": "区间驱动置信水平"
      },
      "min": 0,
      "max": 1,
      "step": 0.01,
      "class": "col-12"
    },
    "rx": {
      "type": "switch",
      "label": {
        "en": "Remove X-chromosome",
        "zh_cn": "移除 X 染色体"
      },
      "class": "col-12 col-md-4"
    },
    "genegistic": {
      "type": "switch",
      "label": {
        "en": "Deletions Sig at Gene level",
        "zh_cn": "基因水平计算缺失显著性"
      },
      "class": "col-12 col-md-4"
    },
    "broad": {
      "type": "switch",
      "label": {
        "en": "Broad-level Analysis",
        "zh_cn": "Broad 水平分析"
      },
      "class": "col-12 col-md-4"
    },
    "armpeel": {
      "type": "switch",
      "label": {
        "en": "Arm-level Peel Off",
        "zh_cn": "臂水平剥离"
      },
      "class": "col-12 col-md-4"
    }
  }
}

tinyscholar

{
  "data": {
    "id": {
      "type": "combobox",
      "required": true,
      "label": "Google Scholar ID",
      "prepend-icon": "mdi-diamond-stone"
    }
  }
}

r-code-flow

{
  "data": {
    "code": {
      "type": "codemirror",
      "required": true,
      "label": "messages.common.code"
    }
  }
}

Core R script

Background plotting script is done by default using R. The code is divided into three blocks: data processing and configuration, plotting, and exporting.

• data
• data2
• data3
• ......

Part of functions：

• return_hiplot_palette_color and return_hiplot_palette return color palettes
• choose_ggplot_theme set ggplot2 theme
• export_single export plotting object

conf is the config field in Data JSON.

opt$outputFilePrefix is the exported directory + prefix, such as /path/output/s.12323, then the path of the generated PDF file is /path/output/s.12323.pdf. By dirname(opt$outputFilePrefix) you can get the result output directory.

Any number of PNG, PDF, HTML, tif files, and an XLSX form file can be generated in this directory, and the download path of the relevant files will be sent to the user as the result.

For tools with more output, a new output directory can be created in the directory as the output path, and the additional results can be packed into a gzip file for download, such as /path/s.12323.tar.gz using the export_directory() function.

# Area
############# Section 1 ##########################
# input options, data and configuration section
##################################################
{
  # rename colnames
  usr_xlab <- colnames(data)[2]
  usr_ylab <- colnames(data)[3]
  colnames(data) <- c("Group", "xvalue", "yvalue")
}

############# Section 2 #############
#           plot section
#####################################
{
  p <- ggplot(data, aes(x = xvalue, y = yvalue, fill = Group)) +
    geom_area(alpha = conf$general$alpha) +
    ylab(usr_ylab) +
    xlab(usr_xlab) +
    ggtitle(conf$general$title)

  ## add color palette
  p <- p + return_hiplot_palette_color(conf$general$palette,
  conf$general$paletteCustom) +
    return_hiplot_palette(conf$general$palette,
  conf$general$paletteCustom)

  theme <- conf$general$theme
  p <- choose_ggplot_theme(p, theme)
}

############# Section 3 #############
#          output section
#####################################
{
  export_single(p)
}

For other command line scripts (Python/Bash, etc.), you can use the following template (you can get the input parameters via conf), where conf$data can contain any input file, and you can get the corresponding input file path via the parse_file_link(conf$data$[your_file_id]$link) function.

############# Section 1 ##########################
# input options, data and configuration section
##################################################
{
  ## Input should be a segmentation file
  if ("data" %in% names(conf) && "input" %in% names(conf$data) &&
    conf$data$input$link != "") {
    infile <- parse_file_link(conf$data$input$link)
  }
}
############# Section 2 #############
#           plot section
#####################################
{
outdir <- sprintf("%s/output", dirname(opt$outputFilePrefix))
outlog <- sprintf("%s/task.log", dirname(opt$outputFilePrefix))
dir.create(outdir)

cmds <- paste("prog",
  "param1",
  "param2",
  "&>>", outlog)
cat(cmds, sep = "\n")
system(cmds)
}

############# Section 3 #############
#          output section
#####################################
{
  owd <- getwd()
  setwd(outdir)
  system(sprintf(
    "tar -czv * -f %s.addition.tar.gz",
    opt$outputFilePrefix
  ))
  src <- list.files(outdir, ".pdf|.png", full.names = TRUE)
  dest <- dirname(opt$outputFilePrefix)
  file.copy(src, dest)
  setwd(owd)
  unlink(outdir, recursive = TRUE)
}