diff --git a/README.md b/README.md index 57eb169f..c0e3944e 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,14 @@ WebGen is hosted on GitHub Pages at [web4bio.github.io/webgen/main/html](https:/ View our May 2020 interactive presentation at [web4bio.github.io/webgen/presentationPoster/](https://web4bio.github.io/webgen/presentationPoster/) -Conference call via [Zoom](https://sbubmi.page.link/vip) Fridays at 11:45AM EST +Conference call via [Zoom](https://stonybrook.zoom.us/j/92985669090?pwd=dER6N0xnZHJxRlpHYmlNVzF6VUJrZz09) W 2:30 - 3:23 PM EST Other weekly meetings [here](https://www.when2meet.com/?12629008-XMsjv) +[Private folder](https://drive.google.com/drive/u/2/folders/1bEpJgpqKHLILIlRFF0ucvlOZr2vJ5knZ) for Spring 2024 student notebooks + ## Background -Precision Medicine requires an ever-growing biomedical big data reference. This growth is particularly striking for pathologies with a genomic basis, like cancer. Accordingly, NIH/NCI has spearheaded the establishment of an interoperable multi-petabyte-sized [Genomic Data Commons](gdc.cancer.gov) ([PMC5683428](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5683428/)) as a data ecosystem that the scientific community, including the citizen-scientist, can populate with analytical applications. The goal of this project is to explore this new data-rich landscape by developing nimble Web applications (apps) that help find novel associations between genomic features and cancer phenotypes. +There is an ever-growing Biomedical BigData reference, which is particularly striking for (1) pathologies with a genomic basis, like Cancer, and (2) observational studies from electronic health records. Accordingly, NIH has spearheaded the establishment of interoperable repositories such as the Genomic Data Commons (gdc.cancer.gov) & the National Covid Cohort Collaborative (covid.cd2h.org). These data ecosystems allow the scientific community, including the citizen scientist, to generate complimentary analytical applications. The goal of this project is to explore this new data-rich landscape by developing nimble Web Applications (Apps) using these public data.. ## How to Contribute @@ -32,17 +34,19 @@ This is a public, open-source project, as well as a project that students may re | --- | --- | --- | --- | | [Richard Moffitt](https://github.com/rmoffitt) | [Folder](/archive/richard/), [js Sandbox](/archive/richard/richard.html) | [Notebook homepage](https://observablehq.com/@rmoffitt?tab=notebooks), [WebGen page](https://observablehq.com/@rmoffitt/webgen), [Simple GDC query tool](https://observablehq.com/@rmoffitt/tcgaplots) | [Faculty website](https://bmi.stonybrookmedicine.edu/people/moffitt_richard) | | [Jonas Almeida](http://www.github.com/jonasalmeida) | [Folder](https://github.com/web4bio/webgen/tree/master/archive/jonas), [js Sandbox](https://web4bio.github.io/webgen/archive/jonas/) | [Sandbox](https://beta.observablehq.com/@jonasalmeida/webgen) | [Firebrowse](https://github.com/episphere/firebrowse) | +| [Alisa Yurovsky](https://github.com/ayurovsky) | | [Observable](https://observablehq.com/@ayurovsky) | [Faculty website](https://ayurovsky.github.io/) | | [Adit Anand](https://github.com/19aanand) | [Spring 2020 Log](https://docs.google.com/document/d/1K6yBJq7C4XOlkl4Hm5smnPiY-lj_lJ2miwV6pRl-KEU/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/1g1pkQcqoDTa40BUXveAWDokW_1Q-spkC_0n6xB5vTO8/edit), [Spring 2021 Log](https://docs.google.com/document/d/1UBOF3QSd02kix0n5uzxW3Eqs1lzMZXHmorj1T8GJ8Cw/edit?usp=sharing), [Fall 2021 Log](https://docs.google.com/document/d/13BsRrLdiGLRID1_ujppGLsEVq2g1U1ffXv8c4kDbia4/edit?usp=sharing) | [Observable](https://observablehq.com/@19aanand), [Spring 2022 Log](https://docs.google.com/document/d/1sAw29x8wT0yNvueq61pPnCzOpuv3ls3LPKOYm_D2UMM/edit?usp=sharing) | | -| [Eric Ruan](https://github.com/ericr491) | [Fall 2020 Log](https://docs.google.com/document/d/1RldOmYmN9yAjB2dhHcvPQdRe_WidyJhlccK51Nb8tL8/edit?usp=sharing) [Spring 2021 Log](https://docs.google.com/document/d/1E57BM8ln0ewCxISpZ9LQnRqD4SuqdmNj42SgI5eLKD4/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/1OpXK8qwvS5juWyJMlgKuINEAMhm28c85loT4u1oMrnc/edit?usp=sharing) [Spring 2022 Log](https://docs.google.com/document/d/1Q3xe8NNM8B3HeSc85a-9e3fAH4NEztp-zrs_Sj0x67o/edit?usp=sharing)| [Sandbox](https://observablehq.com/@ericr491/webgen) | | | [Purva Shenoy](https://github.com/prvshenoy01) |[Spring 2021 Log,](https://docs.google.com/document/d/1vo6JgeLybK2bQZVbIQKpvwXKHdMI1QGGGrPGXOzRIrA/edit?usp=sharing) [Fall 2021 Log,](https://docs.google.com/document/d/1Ku6s_Y_XVSa5IFjgfgdrf_9WD64o_77Q7NmDrRIk_FA/edit?usp=sharing) [Spring 2022 Log](https://docs.google.com/document/d/1Mpy5ksn_UF-2igpojq4JGo0o4BnprAND6CMBtpMlM9w/edit?usp=sharing)| | -| [Jie Xi Li](https://github.com/jli0980) | [Spring 2022 Log](https://docs.google.com/document/d/1NPfO22X5CkfYnU697NwupE9xVAoyIRRuVZ5tCBRg3BI/edit?usp=sharing) |[Observable](https://observablehq.com/@39a49c172bedfa3c/webgen-spring-2022)| | -| [Amara Im](https://github.com/amaraim22) | [Spring 2021 Log](https://docs.google.com/document/d/1L9jJvpQX5DLRC43ajV3Sk4Cll0koJPJI6Uu3oediN1Y/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/19PlE5GM0VXGWPHi2ZcMEAkKjnqIVjut4E2i2n13-ghk/edit?usp=sharing) | [Sandbox](https://observablehq.com/@amaraim22/webgen) | | -| [Erika Nemeth](http://www.github.com/enemeth19) | [Fall 2019 Log](https://docs.google.com/document/d/1yCoHM8SleFvwsuQzfcO19oCWE36EUJ482bX38X8a7xY/edit?usp=sharing), [Spring 2020 Log](https://docs.google.com/document/d/11f0B8j0gTE6leyFeDKHd6onu2LOnVyqPDmGc-vt5d_c/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/18d5oB-Uft5nBskVxnZuEcaXHDPE291y2PBzQtcPZXVo/edit?usp=sharing), [Spring 2021 Log](https://docs.google.com/document/d/1aWkkX9PEcEZWaK37F5n0_LABoo1JIj8OS-mkj4k5Ras/edit?usp=sharing) | [WebGen Background](https://observablehq.com/@enemeth19/webgen) | [Interactive Plots](https://episphere.github.io/mortalitytracker/board/) | -| [Zhenghao (Kevin) Zhu](https://github.com/ZhenghaoZhu) | [Spring 2020 Log](https://docs.google.com/document/d/1x_UYj9iuYBXwfJBVzOtyGaZJc6LOymu_gvBZ-CIJt2U/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/1HMWPe9dYiMrsONfoxObnglpwDLDVDa-Hu2AnJ0bcJmE/edit?usp=sharing) | [Sandbox](https://observablehq.com/@zhenghaozhu/webgen) | | +| [Amara Im](https://github.com/amaraim22) | [Spring 2021 Log](https://docs.google.com/document/d/1L9jJvpQX5DLRC43ajV3Sk4Cll0koJPJI6Uu3oediN1Y/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/19PlE5GM0VXGWPHi2ZcMEAkKjnqIVjut4E2i2n13-ghk/edit?usp=sharing) [Fall 2022 Log](https://docs.google.com/document/d/1ZE97XnPLILWKoFeXxWmpxs0EThEESZzuF5_ljgCdLgs/edit?usp=sharing) [Spring 2023 Log](https://docs.google.com/document/d/1Z6aC6eDo7dA4lz5VcV2YX2gMvIp4f-e86RUH-0jaCxE/edit?usp=sharing) | [Observable](https://observablehq.com/@amaraim22/webgen) | | +| [Erika Nemeth](http://www.github.com/enemeth19) | [Fall 2019 Log](https://docs.google.com/document/d/1yCoHM8SleFvwsuQzfcO19oCWE36EUJ482bX38X8a7xY/edit?usp=sharing), [Spring 2020 Log](https://docs.google.com/document/d/11f0B8j0gTE6leyFeDKHd6onu2LOnVyqPDmGc-vt5d_c/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/18d5oB-Uft5nBskVxnZuEcaXHDPE291y2PBzQtcPZXVo/edit?usp=sharing), [Spring 2021 Log](https://docs.google.com/document/d/1aWkkX9PEcEZWaK37F5n0_LABoo1JIj8OS-mkj4k5Ras/edit?usp=sharing) | [WebGen Background](https://observablehq.com/@enemeth19/webgen) | [Interactive Plots](https://episphere.github.io/mortalitytracker/board/) | | +| [Uday Turakhia](http://www.github.com/udayVT) | [Fall 2023 Log](https://docs.google.com/document/d/1AbRlyMOsLEybLh_TA-AhgaU8z1NMaR_Rq93G8ZzAx8Y/edit?usp=sharing) | [NASA Events API](https://observablehq.com/d/c700b9b021e656ab), [State VS Covid](https://observablehq.com/d/e25947262687ee2d) | | | + + #### Alumni * [Kevin Murgas](https://github.com/kevin-murgas) * [Luke Torre-Healy](https://github.com/lthealy) + * [Eric Ruan](https://github.com/ericr491) :[Sandbox](https://observablehq.com/@ericr491/webgen) * [Chowdhury An-Noor](https://github.com/chowdhuryannoor) * [Yuwei Zhang](https://github.com/Yuw-zhang) * [Soma Kobayashi](https://github.com/skobayashi0417) @@ -67,7 +71,9 @@ This is a public, open-source project, as well as a project that students may re * [Kevin Chang](https://github.com/Xnonx14): [Sandbox](https://beta.observablehq.com/@xnonx14/kevin-changs-notebook) * [Jonathan Krog](https://github.com/Jonathan-Krog): [Sandbox](https://beta.observablehq.com/@jonathan-krog/webgen-fall-2019) * [Chantelle Dsilva](http://www.github.com/chantelle-dsilva): [Sandbox](https://beta.observablehq.com/@chantelle-dsilva/webgen) - + * [Jie Xi Li](https://github.com/jli0980): [Observable](https://observablehq.com/@39a49c172bedfa3c/webgen-spring-2022) + * [Zhenghao (Kevin) Zhu](https://github.com/ZhenghaoZhu) : [Sandbox](https://observablehq.com/@zhenghaozhu/webgen) + ## APIs * GDC https://api.gdc.cancer.gov * [Documentation](https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/#api-endpoints) @@ -92,12 +98,13 @@ ____ - **Interests / Preparation by Major:** Pre-existing knowledge of programming, particularly JavaScript, will be favored as it indicates an innate interest in social coding (user-facing application development). This is applicable to all students, regardless of focus being on Mathematics or Molecular Biology. - **Faculty:** - - Richard Moffitt (Department of Biomedical Informatics) - - Jonas S Almeida (Department of Biomedical Informatics) + - Alisa Yurovsky (Biomedical Informatics, Stony Brook) + - Richard Moffitt (Hematology / Medical Oncology, Biomedical Informatics, Emory University) + - Jonas S Almeida (Naitonal Cancer Institute) - **Team Established:** Spring 2019 -- **Meeting Time:** Friday 11:45am-12:50pm +- **Meeting Time:** W 10:30 -11:25 AM EST - **Meeting Location:** [Zoom](https://sbubmi.page.link/vip) diff --git a/main/css/style.css b/main/css/style.css index 3a3780b0..b7e65baa 100644 --- a/main/css/style.css +++ b/main/css/style.css @@ -1,12 +1,13 @@ /* CSS File for VIP WebGen Site for mRNA-Seq Data Visualization */ -#page-container { +/* #page-container { position: relative; min-height: 160vh; -} +} */ #content-wrap { - padding-bottom: 2.5rem; /* Footer height */ + /* padding-bottom: 2.5rem; */ + min-height: calc(100vh - 2.5rem); } .hide { @@ -20,11 +21,11 @@ /* WebGen Title at top of app */ .PageTitle { - font-family: "Roboto", sans-serif; + font-family: Arial, Helvetica, sans-serif; color: #4db6ac; text-align: center; - font-size: 45px; - font-style: italic; + font-size: 50px; + font-style: bold; margin-bottom: 28px; width: 100%; } @@ -60,12 +61,13 @@ } } -#load{ - width:100%; - height:100%; - position:fixed; - z-index:9999; - background:url("loading-icon-image.gif") no-repeat center center rgba(0,0,0,0.25) +#load { + width: 100%; + height: 100%; + position: fixed; + z-index: 9999; + background: url('loading-icon-image.gif') no-repeat center center + rgba(0, 0, 0, 0.25); } /* ///////////////////////////////////////////////////////////////////////////////////////////////////////////////// */ @@ -128,7 +130,7 @@ /* ///////////////////////////////////////////////////////////////////////////////////////////////////////////////// */ -#geneTwoQuerySelectBox{ +#geneTwoQuerySelectBox { margin-bottom: 10px; margin-top: 10px; text-align: right; @@ -227,9 +229,9 @@ #footer { background-color: #4db6ac; - margin-top: 50%; - position: relative; - bottom: 0; + margin-top: 30px; + /* position: relative; + bottom: 0; */ width: 100%; /* height: 2.5rem; Footer height */ } @@ -246,5 +248,5 @@ font-size: 12px; height: 15px; width: var(--progress); - background-color:#FFDC41; + background-color: #ffdc41; } diff --git a/main/geneList.json b/main/geneList.json deleted file mode 100644 index d721dd2d..00000000 --- a/main/geneList.json +++ /dev/null @@ -1,13344 +0,0 @@ -[ - { - "hugoSymbol": "ABI1", - "entrezGeneId": 10006, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ABL1", - "entrezGeneId": 25, - "oncokbAnnotated": true, - "occurrenceCount": 7, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": true, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "ABL2", - "entrezGeneId": 27, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "ACSL3", - "entrezGeneId": 2181, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ACSL6", - "entrezGeneId": 23305, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ACTB", - "entrezGeneId": 60, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ACTG1", - "entrezGeneId": 71, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "ACVR1", - "entrezGeneId": 90, - "oncokbAnnotated": true, - "occurrenceCount": 4, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "ACVR1B", - "entrezGeneId": 91, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": true, - "foundationHeme": false, - "vogelstein": true, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ACVR2A", - "entrezGeneId": 92, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "AFF1", - "entrezGeneId": 4299, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "AFF3", - "entrezGeneId": 3899, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "AFF4", - "entrezGeneId": 27125, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "AKT1", - "entrezGeneId": 207, - "oncokbAnnotated": true, - "occurrenceCount": 7, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": true, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "AKT2", - "entrezGeneId": 208, - "oncokbAnnotated": true, - "occurrenceCount": 6, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "AKT3", - "entrezGeneId": 10000, - "oncokbAnnotated": true, - "occurrenceCount": 5, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "ALB", - "entrezGeneId": 213, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": true, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ALK", - "entrezGeneId": 238, - "oncokbAnnotated": true, - "occurrenceCount": 7, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": true, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "ALOX12B", - "entrezGeneId": 242, - "oncokbAnnotated": true, - "occurrenceCount": 4, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ANKRD11", - "entrezGeneId": 29123, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "APC", - "entrezGeneId": 324, - "oncokbAnnotated": true, - "occurrenceCount": 7, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": true, - "sangerCGC": true, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "APH1A", - "entrezGeneId": 51107, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "APLNR", - "entrezGeneId": 187, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": true, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": true - }, - { - "hugoSymbol": "APOBEC3B", - "entrezGeneId": 9582, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - 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"foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "ZMYM2", - "entrezGeneId": 7750, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZMYM3", - "entrezGeneId": 9203, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNF217", - "entrezGeneId": 7764, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": true, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNF24", - "entrezGeneId": 7572, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNF331", - "entrezGeneId": 55422, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNF384", - "entrezGeneId": 171017, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNF521", - "entrezGeneId": 25925, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNF703", - "entrezGeneId": 80139, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": true, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZNRF3", - "entrezGeneId": 84133, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": true, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "ZRSR2", - "entrezGeneId": 8233, - "oncokbAnnotated": true, - "occurrenceCount": 5, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - } -] \ No newline at end of file diff --git a/main/html/about.html b/main/html/about.html index 2229ef01..75dd541c 100644 --- a/main/html/about.html +++ b/main/html/about.html @@ -1,6 +1,5 @@ - @@ -8,24 +7,27 @@ - - + - - -
+

About Us

WebGen was created by the WebGen Vertically-Integrated Project team at Stony Brook University. @@ -70,45 +72,65 @@

Alumni
  • Chantelle Dsilva
  • -

    - - + - - - diff --git a/main/html/index.html b/main/html/index.html index c07fbb2b..8ccd1079 100644 --- a/main/html/index.html +++ b/main/html/index.html @@ -1,27 +1,43 @@ - - + + Web Genomics - - + - + + + - - + + - + @@ -30,7 +46,10 @@ - + @@ -38,54 +57,43 @@ -
    - -
    - + -
    - - + +
    -
    -
    -
    - A tool for exploring data from The Cancer Genome Atlas -
    -

    - Currently, this tool enables visualization of gene expression (RNA-seq) data from primary solid tumor - samples via heatmap and violin plot. +

    + 1) Select TCGA solid tumor type(s)

    -
    -
    - -
    -
    - Customize Your Cohort: -
    -
    -
    - -
    -

    1) Select tumor type(s)

    - +

    - 2) Filter data by gene mutation signature and/or by metadata + + 2) Filter by gene mutation signature and/or + metadata +

    -
    " + - "" + - "Hierarchical Clustering" + + "Hierarchical clustering" + ""; sortToggleDiv = sortOptionDiv.append("div") .attr("align", "center") @@ -112,16 +118,21 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d toggleClust = sortToggleDiv.select("#toggleClust") toggleClust.on('change', function () { // function to update state of sortCurrentText and doCluster - sortCurrentText.text(this.checked ? 'hierarchical clustering' : 'mean expression (default)'); + // sortCurrentText.text(this.checked ? 'hierarchical clustering' : 'mean expression (default)'); doCluster = (this.checked ? true : false); sortGroups(); updateHeatmap(); }); + +/////////////////////////////////// +// HEATMAP SETUP +/////////////////////////////////// + ///// BUILD SVG OBJECTS ///// // Set up dimensions for heatmap: var margin = { top: 80, right: 20, space: 5, bottom: 30, left: 50},//100 }, - frameWidth = 1050, + frameWidth = 1200, heatWidth = frameWidth - margin.left - margin.right, legendWidth = 50, heatHeight = 300, @@ -156,6 +167,7 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d svg_frame.append("text") .attr('id', 'heatmapYAxisLabel') + .attr("text-anchor", "start") .style("font-size", "14px") .attr("transform", `translate(15,${yAxisHeight}),rotate(-90)`) .text("Transcripts"); @@ -249,9 +261,18 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d // true : sort by hierarchichal clustering var doCluster = false, clusterReady = false, clust_results, sortOrder, root; function sortGroups() { + if (!data_merge || data_merge.length === 0) { + console.error( + 'data_merge is undefined, null, or empty. Cannot sort groups.' + ); + return; + } if (doCluster && !clusterReady) { // do hierarchical clustering, if not already done (clusterReady) // call clustering function from hclust library - clust_results = clusterData({ data: data_merge, key: 'exps' }); + clust_results = clusterData({ + data: data_merge, + key: 'exps', + }); // re-sort clustering based on average expression within leaves root = d3.hierarchy(clust_results.clusters).sort((a,b) => d3.descending(branchMean(a),branchMean(b))); sortOrder = [].concat.apply([], root.leaves().map(el => el.data.indexes)); @@ -411,7 +432,7 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d ///// Update function for creating plot with new order (clustering), new sample tracks function updateHeatmap() { - // Build new x scale based on borcodes (in case re-sorted) + // Build new x scale based on barcodes (in case re-sorted) x = x.domain(barcodes); // Re/build the heatmap (selecting by custom key 'tcga_id:gene'): @@ -436,7 +457,7 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d let sampTrack_obj = sampTrackVars.map(v => { // get all values for variable v let domain = clinicalAndMutationData.filter(el => (barcodes.includes(el.tcga_participant_barcode))) - .map(d => d[v]).filter(el => el !== "NA").sort(); + .map(d => d[v]).sort(); domain = [...new Set(domain)]; // get unique values only // determine if variable categorical or continuous (numeric) @@ -538,7 +559,7 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d .attr("y", (d, i) => 20 + i * (sampTrackHeight + margin.space)) .attr("width", sampTrackHeight) .attr("height", sampTrackHeight) - .style("fill", d => colorScale_all[v.varname](d)) + .style("fill", d => {if (d == "NA") {return "lightgray"} else {return colorScale_all[v.varname](d)}}) .style("stroke", "black"); svg_sampLegend.selectAll() // add label .data(v.domain, d => v.varname + ":" + d + "_text") @@ -652,4 +673,4 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d svg_frame.attr('height', frameHeight); }; updateHeatmap(); -}; +}; \ No newline at end of file diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index 74db7c29..4c4175c9 100644 --- a/main/js/plots/createPieCharts.js +++ b/main/js/plots/createPieCharts.js @@ -68,7 +68,6 @@ let colorOutOfSpace = { let oldArrayCopy = [...oldArray] const oldDict = colorOutOfSpace.yellowAt[keyName]['Key'] const newDict = colorOutOfSpace.createSliceKey(newListOfSlices) - // console.log({...newDict}) const newKeys = Object.keys(newDict) // scenario occurs when newKeys has less keys than oldKeys @@ -94,7 +93,6 @@ let colorOutOfSpace = { 'YellowAt': oldArrayCopy.filter(ele => ele !== 'X'), 'Key': {...newDict} } - // console.log({...colorOutOfSpace.yellowAt}) }, updateYellowAt: (keyName, sliceToChange) => { const geneDict = colorOutOfSpace.yellowAt[keyName] @@ -125,7 +123,19 @@ let buildDataExplorePlots = async function() { let mySelectedGenes = $('.geneOneMultipleSelection').select2('data').map(clinicalInfo => clinicalInfo.text); let mySelectedClinicalFeatures = $('.clinicalMultipleSelection').select2('data').map(clinicalInfo => clinicalInfo.id); let mySelectedFeatures = mySelectedGenes.concat(mySelectedClinicalFeatures) - + // Remove fields from selectedCategoricalFeatures that were previously selected but now removed + // Iterate over keys of selectedCategoricalFeatures and remove outdated keys + for(let key of Object.keys(selectedCategoricalFeatures)) { + // If one of the keys in selectedCategoricalFeatures is not chosen in one of the select boxes, then remove the key + if(!mySelectedFeatures.includes(key)) + delete selectedCategoricalFeatures[key]; // Delete key, value pair from selectedCategoricalFeatures + } + // Iterate over selectedContinuousFeatures and remove outdated keys + for(let key of Object.keys(selectedContinuousFeatures)) { + // If one of the keys in selectedContinuousFeatures is not chosen in one of the select boxes, then remove the key + if(!mySelectedFeatures.includes(key)) + delete selectedContinuousFeatures[key]; // Delete key, value pair from selectedContinuousFeatures + } // if no features are selected, do not display any pie charts if(mySelectedFeatures.length == 0) { document.getElementById('dataexploration').innerHTML = "" @@ -145,9 +155,6 @@ let buildDataExplorePlots = async function() { } // if unselected feature is not a gene, set isSelected status to false if(unselectedFeature[0] !== unselectedFeature[0].toUpperCase()) { - //DEBUG - console.log("Printing from buildDataExplorePlots() for clinical feature!"); - //DEBUG let index = clinicalType.findIndex(x => x.name == unselectedFeature); clinicalType[index].isSelected = false; } @@ -204,13 +211,13 @@ let buildDataExplorePlots = async function() { // if continuous data range has not yet been added if(selectedContinuousFeatures.findIndex(element => element == currentFeature) == -1){ if(currentFeature != "pathologic_stage") - selectedContinuousFeatures.push(currentFeature); + selectedContinuousFeatures[currentFeature] = []; // Initialize to empty array } if(eventData) { - selectedRange[0] = eventData.range.x[0]; - selectedRange[1] = eventData.range.x[1]; + selectedContinuousFeatures[currentFeature][0] = eventData.range.x[0]; + selectedContinuousFeatures[currentFeature][1] = eventData.range.x[1]; } else - selectedRange = (document.getElementById(currentFeature + 'Div')).layout.xaxis.range; + selectedContinuousFeatures[currentFeature] = (document.getElementById(currentFeature + 'Div')).layout.xaxis.range; }); // Add on click event for pie chart @@ -227,10 +234,12 @@ let buildDataExplorePlots = async function() { slice = data.points[j].label; } if(selectedCategoricalFeatures[currentFeature] != null) { - if(selectedCategoricalFeatures[currentFeature].findIndex(element => element == slice) != -1){ + // Obtain index of slice in array + let sliceIndex = selectedCategoricalFeatures[currentFeature].findIndex(element => element == slice); + if(sliceIndex != -1){ let colorArray = colorOutOfSpace.buildColorCodeKeyArray(uniqueValuesForCurrentFeature) colore[pts] = colorArray[pts]; - selectedCategoricalFeatures[currentFeature].pop(slice); + selectedCategoricalFeatures[currentFeature].splice(sliceIndex, 1); // Call splice() method to remove element } else { selectedCategoricalFeatures[currentFeature].push(slice); colore[pts] = '#FFF34B'; @@ -321,14 +330,14 @@ let setChartDimensions = async function(uniqueValuesForCurrentFeature, currentFe if (windowWidth > threeColLower) { currentFeatureDiv.setAttribute("class", "col s4"); } else if (windowWidth > twoColLower) { - currentFeatureDiv.setAttribute("class", "col s5"); + currentFeatureDiv.setAttribute("class", "col s4"); } else { - currentFeatureDiv.setAttribute("class", "col s7"); + currentFeatureDiv.setAttribute("class", "col s6"); } // set chart height and width if (windowWidth >= (1000)) { - chartHeight = 850; + chartHeight = 400; chartWidth = 400; } else if (windowWidth >= (threeColLower)) { chartHeight = 0.8 * (windowWidth) + 80; @@ -346,16 +355,6 @@ let setChartDimensions = async function(uniqueValuesForCurrentFeature, currentFe chartWidth *= 1.2; legend_location_x = 1.2; legend_location_y = 1; - for (let i = 0; i < uniqueValuesForCurrentFeature.length; i++) { - /* - if (uniqueValuesForCurrentFeature[i].length > 10) { - let shorten = ".."; // ellipses for shortening labels in the string - let stringLength = uniqueValuesForCurrentFeature[i].length; - //replaces the label with its shortened version - uniqueValuesForCurrentFeature[i] = shorten.concat(uniqueValuesForCurrentFeature[i].substring(stringLength-7,stringLength)); - } - */ - } if (windowWidth > threeColLower) windowWidth = 849 * dpr; else if (windowWidth > twoColLower) diff --git a/main/js/plots/createViolinPlot.js b/main/js/plots/createViolinPlot.js index 1068ba3e..6412c86f 100644 --- a/main/js/plots/createViolinPlot.js +++ b/main/js/plots/createViolinPlot.js @@ -35,10 +35,9 @@ const createViolinPlot = async function(dataInput, violinDiv, curPlot, facetByFi var violinCurveColors = []; // Set up the figure dimensions: - //var margin = {top: 10, right: 30, bottom: 30, left: 40}, var margin = {top: 10, right: 30, bottom: 10, left: 40}, width = 505 - margin.left - margin.right, - height = 225 - margin.top - margin.bottom; + height = 200 - margin.top - margin.bottom; // Filter out null values: dataInput = dataInput.filter(patientData => patientData.expression_log2 != null); @@ -179,14 +178,17 @@ const createViolinPlot = async function(dataInput, violinDiv, curPlot, facetByFi var y = d3.scaleLinear() .domain([minExpressionLevel, maxExpressionLevel]) .range([height, 0]); - svgObject.append("g").call( d3.axisLeft(y)); + svgObject.append("g").call( d3.axisLeft(y)) + .style("font-size", "8px"); + //Append y-axis label svgObject.append("text") .attr("transform", "rotate(-90)") - .attr("y", 0 - margin.left) - .attr("x",0 - (height / 1.6)) + .attr("y", -margin.left) + .attr("x",-(height / 2.0)) .attr("dy", "1em") .style("text-anchor", "middle") + .style("font-size", "12px") .text("Expression Level"); // Build and Show the X scale. It is a band scale like for a boxplot: each group has an dedicated RANGE on the axis. This range has a length of x.bandwidth @@ -200,12 +202,13 @@ const createViolinPlot = async function(dataInput, violinDiv, curPlot, facetByFi .call(d3.axisBottom(x)) .selectAll(".tick text") .attr("transform", "rotate(-20), translate(-10, 5)") - .call(wrap, x.bandwidth()); + .call(wrap, x.bandwidth()) + .style("font-size", "8px"); svgObject.append("text") - .attr("transform", "translate(" + width/2 + ", " + (height + margin.top + 30) + ")") - //.style("text-anchor", "middle") - .text('Cohort'); + .attr("transform", "translate(" + width/2 + ", " + (height + margin.top + 50) + ")") + .text("Cohort") + .style("font-size", "12px"); ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// @@ -435,7 +438,7 @@ const createViolinPlot = async function(dataInput, violinDiv, curPlot, facetByFi .attr("x", 0) .attr("y", -25) .attr("text-anchor", "left") - .style("font-size", "22px") + .style("font-size", "12px") .text("Gene Expression Violin Plot for "+ curPlot); }; @@ -514,19 +517,25 @@ function standardDeviation(mean, values) */ let createViolinPartitionBox = async function(partitionDivId, geneQuery) { - var div_box = d3.select('#'+partitionDivId); - div_box.append('text') - .style("font-size", "20px") - .text('Select variables to partition violin curves by:'); + var div_box = d3.select(`#${partitionDivId}`); + div_box + .style('font-size', '14px') + .style('font-weight', 'bold') + .text('Select partition variables') + .attr("class", "col s3") + .style("margin-top", "30px") + .style("margin-left", "20px"); + div_box.append('br') div_box.append('div') .attr('class','viewport') .attr("id", "partitionSelectViolinPlot") .style('overflow-y', 'scroll') - .style('height', '300px') + .style('height', '365px') .style('width', '300px') + .style('text-align', 'left') + .style("font-size", "14px") .append('div') .attr('class','body'); - var selectedText = div_box.append('text'); let div_body = div_box.select('.body'); var choices; @@ -538,33 +547,26 @@ let createViolinPartitionBox = async function(partitionDivId, geneQuery) let cb = d3.select(this); if(cb.property('checked')){ choices.push(cb.property('value')); }; }); - - if(choices.length > 0){ selectedText.text('Selected: ' + choices.join(', ')); } - else { selectedText.text('None selected'); }; } // function to create a pair of checkbox and text - function renderCB(div_obj, data) - { - const label = div_obj.append('div').attr('id', data); - - label.append("label") - .attr("class", "switch") - .append("input") + function renderCB(div_obj, data) { + const label = div_obj.append('div') + const label2 = label.append("label") + label2.append("input") + .attr('id', data) .attr("class", "myViolinCheckbox") .attr("value", data) .attr("type", "checkbox") .on('change', function () { update(); rebuildViolinPlot(partitionDivId, geneQuery); - }) - .attr("style", 'opacity: 1; position: relative; pointer-events: all') - .append("span") - .attr("class", "slider round") - .attr('value', data); - - label.append('text') - .text(data); + }); + + label2.append("span") + .text(' ' + data) + .style('font-weight', 'normal') + .style("color", "#5f5f5f"); } // data to input = clinical vars from query diff --git a/main/js/smartCache/main.js b/main/js/smartCache/main.js index 4904d484..ad8fa60c 100644 --- a/main/js/smartCache/main.js +++ b/main/js/smartCache/main.js @@ -317,7 +317,7 @@ function CacheInterface(nameOfDb) { * @param {Map} interface * @returns */ - function constructQueriesGE(listOfCohorts, listOfGenes, listOfBarcodes = [], interface) { + async function constructQueriesGE(listOfCohorts, listOfGenes, listOfBarcodes = [], interface) { /*There is no scenario in which a subset of a cohort's gene expression data gets cached before the entire cohort's gene expression data is cached.*/ let res = {} @@ -341,9 +341,15 @@ function CacheInterface(nameOfDb) { //Within the empty JSON referenced by res[cohort], append gene as a property that points to empty array res[cohort][gene] = []; } + //Obtain list of barcodes with cacheBAR + let cacheBAR = await getCacheBAR(); + //Retrieve an array of Maps linking cohorts to their set of TCGA barcodes + let cohortBarcodes = (await cacheBAR.fetchWrapperBAR(listOfCohorts = [cohort]))[0].barcodes; + //Get the barcodes being requested for the current cohort + cohortBarcodesOfInterest = listOfBarcodes.filter(barcode => cohortBarcodes.includes(barcode)); /*If a listOfBarcodes contains data, then identify the barcodes that are not cached for a cohort, gene combination and identify the barcodes that are cached for a cohort, gene combination. */ - let [diff, alreadyHave] = findDiff(listOfBarcodes, cohort, gene, interface) + let [diff, alreadyHave] = findDiff(cohortBarcodesOfInterest, cohort, gene, interface) if (diff.size > 0) { diff.forEach((val) => res[cohort][gene].push(val)) } @@ -357,7 +363,7 @@ function CacheInterface(nameOfDb) { //If no genes are cached for a certain cohort at all, then delete the JSON field for cohort from res if(Object.keys(foundRes[cohort]).length === 0) delete foundRes[cohort] - } + } for (let cohort in res) { //If no genes are cached for a certain cohort at all, then delete the JSON field for cohort from res if(Object.keys(res[cohort]).length === 0) @@ -394,7 +400,7 @@ function CacheInterface(nameOfDb) { } //Identify missing gene expression records and retrieve currently-cached gene expression records - let [missingInterface, hasInterface] = constructQueriesGE(listOfCohorts, listOfGenes, listOfBarcodes, this.interface) + let [missingInterface, hasInterface] = await constructQueriesGE(listOfCohorts, listOfGenes, listOfBarcodes, this.interface) //tmp will store an array of JSON objects let tmp = [] @@ -430,15 +436,24 @@ function CacheInterface(nameOfDb) { let cacheBAR = await getCacheBAR(); // Obtain list of barcodes with cacheBAR let currentListOfBarcodes = await cacheBAR.fetchWrapperBAR([cohort]); // Retrieve an array of Maps linking cohorts to their set of TCGA barcodes currentListOfBarcodes = currentListOfBarcodes[0].barcodes; // Since we are only requesting one barcode at a time, we can index the first element to retrieve the desired barcodes array - //Within a cohort, iterate over each gene that the caching interface retrieved mRNA_Seq data for with executeQueriesGE() - for (let gene of Object.keys(missingInterface[cohort])) { - for (let curBarcode of currentListOfBarcodes) { - //If there are specific barcodes we are requesting, then return only those barcodes' gene expression data - if(listOfBarcodes && listOfBarcodes.includes(curBarcode)) - tmp.push(interfaceData.get(gene).get(curBarcode)); - //If there are no specific barcodes we are requesting, then do not use filter - else if(!listOfBarcodes) - tmp.push(interfaceData.get(gene).get(curBarcode)); + + for (geneObj of interfaceData) { + //First element in geneObj is the gene name + gene = geneObj[0] + //Second element in geneObj is map TCGA barcodes to TCGA expression records + expressionMap = geneObj[1] + for(expressionObj of expressionMap) { + //First element in expressionObj is patient's TCGA barcode + let barcode = expressionObj[0]; + //If there is a subset of barcodes being requested, apply that filter + if(listOfBarcodes && listOfBarcodes.includes(barcode)) { + //Second element in expressionObj is the mRNA_Seq information for current patient + tmp.push(expressionObj[1]); + } + //If no subset of barcodes is being requested, then do not apply a filter + else if(!listOfBarcodes) { + tmp.push(expressionObj[1]) + } } } } @@ -737,6 +752,11 @@ function CacheInterface(nameOfDb) { } async function executeQueriesCLIN(barcodesByCohort, interface) { + $( + '.clinicalMultipleSelection, .pathwayMultipleSelection' + ) + .prop('disabled', true) + .trigger('change.select2'); for (let cohort in interface) { let getBarcodesInACohort = barcodesByCohort.filter(cohortEle => (cohortEle.cohort == cohort))[0].barcodes let clinicalData = await firebrowse.fetchClinicalFH({ @@ -754,6 +774,11 @@ function CacheInterface(nameOfDb) { return undefined }); } + $( + '.clinicalMultipleSelection, .pathwayMultipleSelection' + ) + .prop('disabled', false) + .trigger('change.select2'); } let [missingInterface, hasInterface] = constructQueriesCLIN(listOfCohorts, this.interface) @@ -773,7 +798,6 @@ function CacheInterface(nameOfDb) { } await executeQueriesCLIN(barcodesByCohort, missingInterface); - console.log(missingInterface) for(let cohort in missingInterface) { let newClinicalData = await this.interface.get(cohort);