From 4a013cc47f7190ce96ee9ddb874cf7ab1e273cdd Mon Sep 17 00:00:00 2001 From: Richard Moffitt Date: Mon, 22 Aug 2022 18:34:30 -0400 Subject: [PATCH 01/44] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 57eb169f..7147e813 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ 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://sbubmi.page.link/vip) Wednesdays at 9:15AM EST Other weekly meetings [here](https://www.when2meet.com/?12629008-XMsjv) ## Background From 482a711d2e47214f642d347e383dcb33284f4bae Mon Sep 17 00:00:00 2001 From: Richard Moffitt Date: Tue, 24 Jan 2023 12:19:39 -0500 Subject: [PATCH 02/44] Update README.md --- README.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 7147e813..75d15578 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,12 @@ 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) Wednesdays at 9:15AM EST +Conference call via [Zoom](https://sbubmi.page.link/vip) W 10:30 -11:25 AM EST Other weekly meetings [here](https://www.when2meet.com/?12629008-XMsjv) ## 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 @@ -35,10 +35,9 @@ This is a public, open-source project, as well as a project that students may re | [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) | | + #### Alumni * [Kevin Murgas](https://github.com/kevin-murgas) @@ -67,7 +66,9 @@ 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 +93,13 @@ ____ - **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) From fa6774cbd46df53c77a5b82ddb259d48995938c6 Mon Sep 17 00:00:00 2001 From: Richard Moffitt Date: Wed, 8 Feb 2023 10:28:52 -0500 Subject: [PATCH 03/44] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 75d15578..56bc288b 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,8 @@ View our May 2020 interactive presentation at [web4bio.github.io/webgen/presenta Conference call via [Zoom](https://sbubmi.page.link/vip) W 10:30 -11:25 AM EST Other weekly meetings [here](https://www.when2meet.com/?12629008-XMsjv) +[Private folder](https://drive.google.com/drive/u/1/folders/1LHkly4auVYhwcCb1xAUr-x9BkIluDVN8) for 2023 student notebooks + ## Background 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.. From 0585a71406b7d0bcf813d13cf8c12ff8b79f7c85 Mon Sep 17 00:00:00 2001 From: Richard Moffitt Date: Wed, 8 Feb 2023 10:41:35 -0500 Subject: [PATCH 04/44] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 56bc288b..96e5c445 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ View our May 2020 interactive presentation at [web4bio.github.io/webgen/presenta Conference call via [Zoom](https://sbubmi.page.link/vip) W 10:30 -11:25 AM EST Other weekly meetings [here](https://www.when2meet.com/?12629008-XMsjv) -[Private folder](https://drive.google.com/drive/u/1/folders/1LHkly4auVYhwcCb1xAUr-x9BkIluDVN8) for 2023 student notebooks +[Private folder](https://drive.google.com/drive/u/1/folders/1_ojgzW8VkjHMVdbd4wMM9cjAiC4QKpQ5) for 2023 student notebooks ## Background From b7674543d8ef6934035cf093fd83929ddb0e53a1 Mon Sep 17 00:00:00 2001 From: Amara Im Date: Wed, 8 Feb 2023 10:54:48 -0500 Subject: [PATCH 05/44] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 96e5c445..92807ed5 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ This is a public, open-source project, as well as a project that students may re | [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)| | -| [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) | | +| [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/) | From 8c70df495bb1e47c756ea7495c5664b4ceedde28 Mon Sep 17 00:00:00 2001 From: ayurovsky Date: Wed, 8 Feb 2023 11:26:20 -0500 Subject: [PATCH 06/44] Update README.md Let's try this again --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 92807ed5..d9d532f2 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,7 @@ 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) | | | [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)| | From 39fab58333245825cf0fc572ff28d208d36d9f6e Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Tue, 18 Jul 2023 12:32:49 -0400 Subject: [PATCH 07/44] Fixed JSON file being used to populate second gene select box --- main/js/fillSelectBoxes.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main/js/fillSelectBoxes.js b/main/js/fillSelectBoxes.js index d9a438af..e3b32f42 100644 --- a/main/js/fillSelectBoxes.js +++ b/main/js/fillSelectBoxes.js @@ -135,7 +135,7 @@ let displayNumberSamples = async function () { */ let getValidGeneList = async function () { let validGeneList = await fetch( - "https://web4bio.github.io/webgen/main/geneList.json" + "https://web4bio.github.io/webgen/main/validGeneList.json" ).then((response) => response.json()); validGeneList = validGeneList.map((geneInfo) => geneInfo.hugoSymbol); return await validGeneList; From 794ea95f1edd52a6ef69c7b9eaa992b7d0043a87 Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Tue, 18 Jul 2023 15:57:36 -0400 Subject: [PATCH 08/44] Delete geneList.json --- main/geneList.json | 13344 ------------------------------------------- 1 file changed, 13344 deletions(-) delete mode 100644 main/geneList.json 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, - 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"foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "TYK2", - "entrezGeneId": 7297, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": false, - "mSKHeme": true, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "TYRO3", - "entrezGeneId": 7301, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": true, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "U2AF1", - "entrezGeneId": 7307, - "oncokbAnnotated": true, - "occurrenceCount": 7, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": true, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "U2AF2", - "entrezGeneId": 11338, - 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- "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "USP8", - "entrezGeneId": 9101, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": true, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "VAV1", - "entrezGeneId": 7409, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "VAV2", - "entrezGeneId": 7410, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "VEGFA", - "entrezGeneId": 7422, - "oncokbAnnotated": true, - "occurrenceCount": 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false - }, - { - "hugoSymbol": "WDR90", - "entrezGeneId": 197335, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "WIF1", - "entrezGeneId": 11197, - "oncokbAnnotated": true, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "WRN", - "entrezGeneId": 7486, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "WT1", - "entrezGeneId": 7490, - "oncokbAnnotated": true, - "occurrenceCount": 7, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": true, - "sangerCGC": true, - "oncogene": true, - "tsg": true - }, - { - "hugoSymbol": "WWTR1", - "entrezGeneId": 25937, - "oncokbAnnotated": true, - "occurrenceCount": 4, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "XBP1", - "entrezGeneId": 7494, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": false, - "mSKHeme": true, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "XIAP", - "entrezGeneId": 331, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "XPA", - "entrezGeneId": 7507, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "XPC", - "entrezGeneId": 7508, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "XPO1", - "entrezGeneId": 7514, - "oncokbAnnotated": true, - "occurrenceCount": 6, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "XRCC2", - "entrezGeneId": 7516, - "oncokbAnnotated": true, - "occurrenceCount": 4, - "mSKImpact": true, - "mSKHeme": true, - "foundation": true, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "YAP1", - "entrezGeneId": 10413, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "YES1", - "entrezGeneId": 7525, - "oncokbAnnotated": true, - "occurrenceCount": 3, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "YPEL5", - "entrezGeneId": 51646, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "YWHAE", - "entrezGeneId": 7531, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "YY1", - "entrezGeneId": 7528, - "oncokbAnnotated": true, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": false - }, - { - "hugoSymbol": "YY1AP1", - "entrezGeneId": 55249, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZBTB16", - "entrezGeneId": 7704, - "oncokbAnnotated": false, - "occurrenceCount": 2, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": true, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZBTB20", - "entrezGeneId": 26137, - "oncokbAnnotated": true, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": true, - "tsg": true - }, - { - "hugoSymbol": "ZBTB7A", - "entrezGeneId": 51341, - "oncokbAnnotated": false, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": false, - "oncogene": false, - "tsg": false - }, - { - "hugoSymbol": "ZFHX3", - "entrezGeneId": 463, - "oncokbAnnotated": true, - "occurrenceCount": 4, - "mSKImpact": true, - "mSKHeme": true, - "foundation": false, - "foundationHeme": false, - "vogelstein": false, - "sangerCGC": true, - "oncogene": false, - "tsg": true - }, - { - "hugoSymbol": "ZFP36L1", - "entrezGeneId": 677, - "oncokbAnnotated": true, - "occurrenceCount": 1, - "mSKImpact": false, - "mSKHeme": false, - "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 From 2dcd7435e7006808dfa58c9998264efbde61d0c8 Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Thu, 20 Jul 2023 15:06:45 -0400 Subject: [PATCH 09/44] Previous categorical feature filters do not persist after deselecting feature from select box --- main/js/plots/createPieCharts.js | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index 74db7c29..63609355 100644 --- a/main/js/plots/createPieCharts.js +++ b/main/js/plots/createPieCharts.js @@ -125,7 +125,13 @@ 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 mySelectedFeatures and remove outdated keys from selectedCategoricalFeatures + for(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 from selectedCategoricalFeatures + if(!mySelectedFeatures.includes(key)) + delete selectedCategoricalFeatures[key]; // Delete key, value pair from selectedCategoricalFeatures + } // if no features are selected, do not display any pie charts if(mySelectedFeatures.length == 0) { document.getElementById('dataexploration').innerHTML = "" From 57a6a03a9fc30f91559df75516f07d8c949f15e1 Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Thu, 20 Jul 2023 16:05:37 -0400 Subject: [PATCH 10/44] Continuous feature filters now do not persist after feature is deselected --- .../getDataFromSelectedPieSectors.js | 6 ++---- main/js/plots/createPieCharts.js | 21 ++++++++++++------- 2 files changed, 16 insertions(+), 11 deletions(-) diff --git a/main/js/dataAcquisition/getDataFromSelectedPieSectors.js b/main/js/dataAcquisition/getDataFromSelectedPieSectors.js index 65ca226b..a7252a2a 100644 --- a/main/js/dataAcquisition/getDataFromSelectedPieSectors.js +++ b/main/js/dataAcquisition/getDataFromSelectedPieSectors.js @@ -58,10 +58,8 @@ getBarcodesFromSelectedPieSectors = async function(selectedTumorTypes) { } } // loop through all range data - for(let i = 0; i < selectedContinuousFeatures.length; i++) { - let continuousFeature = selectedContinuousFeatures[i]; - let rangeValue = selectedRange; - + for(let continuousFeature of Object.keys(selectedContinuousFeatures)) { + let rangeValue = selectedContinuousFeatures[continuousFeature]; // Get range of data to filter clinicalData by filteredRangeData = clinicalData.filter(person => (person[continuousFeature] >= rangeValue[0] && person[continuousFeature] <= rangeValue[1])) let onlyBarcodes = filteredRangeData.map(x => x.tcga_participant_barcode); diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index 63609355..948b325c 100644 --- a/main/js/plots/createPieCharts.js +++ b/main/js/plots/createPieCharts.js @@ -126,12 +126,18 @@ let buildDataExplorePlots = async function() { 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 mySelectedFeatures and remove outdated keys from selectedCategoricalFeatures - for(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 from selectedCategoricalFeatures + // 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 = "" @@ -210,13 +216,14 @@ 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 + //selectedContinuousFeatures.push(currentFeature); } 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 From 564444b367757e1ba952f41450681610b700fa97 Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Thu, 20 Jul 2023 16:10:24 -0400 Subject: [PATCH 11/44] Removed commented out lines and extraneous console.log() statements --- .../getDataFromSelectedPieSectors.js | 6 ------ main/js/fillSelectBoxes.js | 20 ------------------- main/js/plots/createPieCharts.js | 6 ------ 3 files changed, 32 deletions(-) diff --git a/main/js/dataAcquisition/getDataFromSelectedPieSectors.js b/main/js/dataAcquisition/getDataFromSelectedPieSectors.js index a7252a2a..4ecd79d5 100644 --- a/main/js/dataAcquisition/getDataFromSelectedPieSectors.js +++ b/main/js/dataAcquisition/getDataFromSelectedPieSectors.js @@ -77,7 +77,6 @@ getBarcodesFromSelectedPieSectors = async function(selectedTumorTypes) { // Get intersection of barcodes from selected pie sectors - // console.log(concatFilteredBarcodes) let clicked_gene_mutation = Object.keys(concatFilteredBarcodes); let intersectedBarcodes; @@ -96,11 +95,6 @@ getBarcodesFromSelectedPieSectors = async function(selectedTumorTypes) { intersectedBarcodes = barcodesForCurrentGene.filter(x => barcodesForNextGene.includes(x)); } } - - //DEBUG - //console.log("Final Cohort Size: "); - //console.log(intersectedBarcodes.length) - //DEBUG return intersectedBarcodes } diff --git a/main/js/fillSelectBoxes.js b/main/js/fillSelectBoxes.js index e3b32f42..18a9a708 100644 --- a/main/js/fillSelectBoxes.js +++ b/main/js/fillSelectBoxes.js @@ -266,11 +266,6 @@ let getClinicalByCohortWithMrnaseq = async function () { results.push(clinicalData[index]) } } - - console.log(results) - - // results = await firebrowse.fetchClinicalFH({cohorts: selectedTumorTypes, barcodes: allBarcodes}); - return results; }; @@ -384,7 +379,6 @@ let fillViolinPartitionBox = async function(id) div_box.append('text') .style("font-size", "20px") .text('Select variables to partition violin curves by:'); - console.log(div_box); div_box.append('div') .attr('class','viewport') .style('overflow-y', 'scroll') @@ -413,20 +407,7 @@ let fillViolinPartitionBox = async function(id) // function to create a pair of checkbox and text function renderCB(div_obj, data) { - /* - const label = div_obj.append('div').attr('id', data.id); - label.append('input') - .attr('type', 'checkbox') - .attr('class', 'myCheckbox') - .attr('value', data.id) - .on('change',update) - //.property('checked',true) - label.append('text') - .text(data.id); - */ - const label = div_obj.append('div').attr('id', data); - label.append("label") .attr("class", "switch") .append("input") @@ -438,7 +419,6 @@ let fillViolinPartitionBox = async function(id) .append("span") .attr("class", "slider round") .attr('value', data); - label.append('text') .text(data); } diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index 948b325c..ab4c59c6 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] @@ -157,9 +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; } @@ -217,7 +212,6 @@ let buildDataExplorePlots = async function() { if(selectedContinuousFeatures.findIndex(element => element == currentFeature) == -1){ if(currentFeature != "pathologic_stage") selectedContinuousFeatures[currentFeature] = []; // Initialize to empty array - //selectedContinuousFeatures.push(currentFeature); } if(eventData) { selectedContinuousFeatures[currentFeature][0] = eventData.range.x[0]; From cc91dfd4bfc32824e0a4c4a42d58da8de5fcb61c Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Tue, 1 Aug 2023 10:47:13 -0400 Subject: [PATCH 12/44] Pie charts now have ideal spacing between title and pie sectors --- main/js/plots/createPieCharts.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index ab4c59c6..01aefb3f 100644 --- a/main/js/plots/createPieCharts.js +++ b/main/js/plots/createPieCharts.js @@ -335,7 +335,8 @@ let setChartDimensions = async function(uniqueValuesForCurrentFeature, currentFe // set chart height and width if (windowWidth >= (1000)) { - chartHeight = 850; + //chartHeight = 850; + chartHeight = 400; chartWidth = 400; } else if (windowWidth >= (threeColLower)) { chartHeight = 0.8 * (windowWidth) + 80; @@ -371,6 +372,8 @@ let setChartDimensions = async function(uniqueValuesForCurrentFeature, currentFe legend_location_x = 0; legend_location_y = 1; } + console.log("Legend X-Position:", legend_location_x); + console.log("Legend Y-Position: ", legend_location_y); return [chartHeight, chartWidth, legend_location_x, legend_location_y] } From 4059e013d974fcd8ed10c72aa71d845072466b31 Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Tue, 1 Aug 2023 11:28:04 -0400 Subject: [PATCH 13/44] Made array of clinical features that should be considered continuous --- main/js/fillSelectBoxes.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/main/js/fillSelectBoxes.js b/main/js/fillSelectBoxes.js index 18a9a708..9ea2875b 100644 --- a/main/js/fillSelectBoxes.js +++ b/main/js/fillSelectBoxes.js @@ -339,7 +339,9 @@ let fillClinicalSelectBox = async function () { var nullCount = continuousMap.filter(x => x == null).length; var totalCount = continuousMap.length; var percentContinuous = nullCount / totalCount; - if((percentContinuous < 0.75 && (currentFeature != 'vital_status')) || currentFeature === "days_to_death" || currentFeature === "cervix_suv_results") + let continuousFeaturesArr = ["days_to_death", "cervix_suv_results", "days_to_last_followup", "date_of_initial_pathologic_diagnosis", "number_of_lymph_nodes", "years_to_birth"]; // Array of features that should be considered continuous + if((percentContinuous < 0.75 && (currentFeature != 'vital_status')) || continuousFeaturesArr.includes(currentFeature))/* currentFeature === "days_to_death" || currentFeature === "cervix_suv_results" || + currentFeature === "days_to_last_followup" || currentFeature === "date_of_initial_pathologic_diagnosis")*/ temp.type = "continuous"; else temp.type = "categorical"; From 8523689d8e3e025b89b3596fa8ba570461a17e3e Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Tue, 1 Aug 2023 17:09:19 -0400 Subject: [PATCH 14/44] Added new continuous clinical features for pie charts --- main/js/fillSelectBoxes.js | 5 ++--- main/js/plots/createPieCharts.js | 13 ------------- 2 files changed, 2 insertions(+), 16 deletions(-) diff --git a/main/js/fillSelectBoxes.js b/main/js/fillSelectBoxes.js index 9ea2875b..fe248b6c 100644 --- a/main/js/fillSelectBoxes.js +++ b/main/js/fillSelectBoxes.js @@ -339,9 +339,8 @@ let fillClinicalSelectBox = async function () { var nullCount = continuousMap.filter(x => x == null).length; var totalCount = continuousMap.length; var percentContinuous = nullCount / totalCount; - let continuousFeaturesArr = ["days_to_death", "cervix_suv_results", "days_to_last_followup", "date_of_initial_pathologic_diagnosis", "number_of_lymph_nodes", "years_to_birth"]; // Array of features that should be considered continuous - if((percentContinuous < 0.75 && (currentFeature != 'vital_status')) || continuousFeaturesArr.includes(currentFeature))/* currentFeature === "days_to_death" || currentFeature === "cervix_suv_results" || - currentFeature === "days_to_last_followup" || currentFeature === "date_of_initial_pathologic_diagnosis")*/ + let continuousFeaturesArr = ["days_to_death", "cervix_suv_results", "days_to_last_followup", "date_of_initial_pathologic_diagnosis", "number_of_lymph_nodes", "years_to_birth", "karnofsky_performance_score"]; // Array of features that should be considered continuous + if((percentContinuous < 0.75 && (currentFeature != 'vital_status')) || continuousFeaturesArr.includes(currentFeature)) temp.type = "continuous"; else temp.type = "categorical"; diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index 01aefb3f..6490c4d2 100644 --- a/main/js/plots/createPieCharts.js +++ b/main/js/plots/createPieCharts.js @@ -335,7 +335,6 @@ let setChartDimensions = async function(uniqueValuesForCurrentFeature, currentFe // set chart height and width if (windowWidth >= (1000)) { - //chartHeight = 850; chartHeight = 400; chartWidth = 400; } else if (windowWidth >= (threeColLower)) { @@ -354,16 +353,6 @@ 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) @@ -372,8 +361,6 @@ let setChartDimensions = async function(uniqueValuesForCurrentFeature, currentFe legend_location_x = 0; legend_location_y = 1; } - console.log("Legend X-Position:", legend_location_x); - console.log("Legend Y-Position: ", legend_location_y); return [chartHeight, chartWidth, legend_location_x, legend_location_y] } From 7fc3f206112767269ae7186c539dac3f71998e2a Mon Sep 17 00:00:00 2001 From: Adit Anand Date: Mon, 7 Aug 2023 11:47:11 -0400 Subject: [PATCH 15/44] Pie chart sector selection works properly when deselecting sectors --- main/js/plots/createPieCharts.js | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/main/js/plots/createPieCharts.js b/main/js/plots/createPieCharts.js index ab4c59c6..2fc00cc6 100644 --- a/main/js/plots/createPieCharts.js +++ b/main/js/plots/createPieCharts.js @@ -234,10 +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'; From 7dab3a47012e3ae7ca94ea5d2a9b41af0a8cdc44 Mon Sep 17 00:00:00 2001 From: ayurovsky Date: Wed, 6 Sep 2023 13:57:50 -0400 Subject: [PATCH 16/44] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d9d532f2..ecf2a53b 100644 --- a/README.md +++ b/README.md @@ -6,10 +6,10 @@ 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) W 10:30 -11:25 AM EST +Conference call via [Zoom](https://stonybrook.zoom.us/j/92985669090?pwd=dER6N0xnZHJxRlpHYmlNVzF6VUJrZz09) W 2:00 - 2:55 PM EST Other weekly meetings [here](https://www.when2meet.com/?12629008-XMsjv) -[Private folder](https://drive.google.com/drive/u/1/folders/1_ojgzW8VkjHMVdbd4wMM9cjAiC4QKpQ5) for 2023 student notebooks +[Private folder](https://drive.google.com/drive/u/3/folders/1_9Met_rPigs-GvSKfcV2AH4fOJKW06Wl) for Fall 2023 student notebooks ## Background From 91dc153ada59194aa353228e3e9da64071af8a06 Mon Sep 17 00:00:00 2001 From: Uday Turakhia <115325925+UdayVT@users.noreply.github.com> Date: Tue, 26 Sep 2023 22:52:40 -0400 Subject: [PATCH 17/44] Update README.md (Adding myself to participants table) --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ecf2a53b..24dcdbb9 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,9 @@ This is a public, open-source project, as well as a project that students may re | [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)| | | [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/) | +| [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/@enemeth19/webgen](https://observablehq.com/d/c700b9b021e656ab)) | | | + #### Alumni From 1aff7f8e0204276c437c28ffdb6de9e568d22fc3 Mon Sep 17 00:00:00 2001 From: Uday Turakhia <115325925+UdayVT@users.noreply.github.com> Date: Mon, 2 Oct 2023 18:25:54 -0400 Subject: [PATCH 18/44] Update README.md (adding Uday Turakhia to participants) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 24dcdbb9..fe880e75 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,7 @@ This is a public, open-source project, as well as a project that students may re | [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)| | | [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/@enemeth19/webgen](https://observablehq.com/d/c700b9b021e656ab)) | | | +| [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) | | | From 4d40a11d963a616e0c7f54d3e54d42354b4fc8db Mon Sep 17 00:00:00 2001 From: Uday Turakhia <115325925+UdayVT@users.noreply.github.com> Date: Wed, 8 Nov 2023 14:47:42 -0500 Subject: [PATCH 19/44] Update README.md with State VS Covid notebook --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fe880e75..acdc97a5 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,7 @@ This is a public, open-source project, as well as a project that students may re | [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)| | | [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) | | | +| [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) | | | From b554ab8bd37f17bed0bb3991e8d85f9a446b98fb Mon Sep 17 00:00:00 2001 From: ayurovsky Date: Fri, 26 Jan 2024 21:36:48 -0500 Subject: [PATCH 20/44] Update README.md for Spring 2024 --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ecf2a53b..fdddda29 100644 --- a/README.md +++ b/README.md @@ -6,10 +6,10 @@ 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://stonybrook.zoom.us/j/92985669090?pwd=dER6N0xnZHJxRlpHYmlNVzF6VUJrZz09) W 2:00 - 2:55 PM 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/3/folders/1_9Met_rPigs-GvSKfcV2AH4fOJKW06Wl) for Fall 2023 student notebooks +[Private folder](https://drive.google.com/drive/u/2/folders/1bEpJgpqKHLILIlRFF0ucvlOZr2vJ5knZ) for Spring 2024 student notebooks ## Background From e3125edd84a03eda6c2c5e414e2488ecfe2620f8 Mon Sep 17 00:00:00 2001 From: ayurovsky Date: Fri, 2 Feb 2024 13:53:28 -0500 Subject: [PATCH 21/44] Update README.md added faculty website --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fdddda29..defdbf88 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ 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) | | +| [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)| | From 058cc40b4ceff098616c627b7b002077ff1e8702 Mon Sep 17 00:00:00 2001 From: Richard Moffitt Date: Wed, 7 Feb 2024 14:48:14 -0500 Subject: [PATCH 22/44] RM Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 57cdd3b2..c0e3944e 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,6 @@ This is a public, open-source project, as well as a project that students may re | [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)| | | [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/) | | @@ -47,6 +46,7 @@ This is a public, open-source project, as well as a project that students may re #### 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) From 195ccd7c062086548dad4fe7240ec87e540fcf68 Mon Sep 17 00:00:00 2001 From: DongPing Lian Date: Wed, 3 Apr 2024 14:37:32 -0400 Subject: [PATCH 23/44] Added error checking for data_merge is defined in sortGroups() --- main/js/plots/createHeatmap.js | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/main/js/plots/createHeatmap.js b/main/js/plots/createHeatmap.js index c8048fc0..56757d10 100644 --- a/main/js/plots/createHeatmap.js +++ b/main/js/plots/createHeatmap.js @@ -249,6 +249,12 @@ 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' }); From 140e125e722a3c1a9f2105434168ee8f45b5b1fe Mon Sep 17 00:00:00 2001 From: DongPing Lian Date: Wed, 3 Apr 2024 14:41:18 -0400 Subject: [PATCH 24/44] Render Sections 2 and 3 hidden until tumor type fetch processes --- main/html/index.html | 16 ++++++++++++++-- main/js/smartCache/main.js | 2 ++ 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/main/html/index.html b/main/html/index.html index c07fbb2b..a5735bf6 100644 --- a/main/html/index.html +++ b/main/html/index.html @@ -93,7 +93,12 @@
@@ -319,7 +324,8 @@
{ + cohorts = $(".cancerTypeMultipleSelection").select2("data"); + $(".geneOneMultipleSelection, .clinicalMultipleSelection, .geneTwoMultipleSelection, .pathwayMultipleSelection") + .prop("disabled", true).trigger("change.select2"); + + } diff --git a/main/js/smartCache/main.js b/main/js/smartCache/main.js index 4904d484..03d3dac2 100644 --- a/main/js/smartCache/main.js +++ b/main/js/smartCache/main.js @@ -754,6 +754,8 @@ function CacheInterface(nameOfDb) { return undefined }); } + $(".geneOneMultipleSelection, .clinicalMultipleSelection, .geneTwoMultipleSelection, .pathwayMultipleSelection") + .prop("disabled", false).trigger("change.select2"); } let [missingInterface, hasInterface] = constructQueriesCLIN(listOfCohorts, this.interface) From e45c55e7a7529b897205a6182328203682f5f03a Mon Sep 17 00:00:00 2001 From: DongPing Lian Date: Wed, 3 Apr 2024 14:42:42 -0400 Subject: [PATCH 25/44] Added progress bar for clustering heatmap --- main/js/plots/createHeatmap.js | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/main/js/plots/createHeatmap.js b/main/js/plots/createHeatmap.js index 56757d10..4663ae73 100644 --- a/main/js/plots/createHeatmap.js +++ b/main/js/plots/createHeatmap.js @@ -255,15 +255,30 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d ); return; } - if (doCluster && !clusterReady) { // do hierarchical clustering, if not already done (clusterReady) + if (doCluster && !clusterReady) { // do hierarchical clustering, if not already done (clusterReady)\ + ProgressBar.setPercentage(0, 'Beginning cluster'); + + // update the progress bar + const onClusteringProgress = (progress) => { + const overallProgress = progress * 100; // Since there are 2 phases, each contributes 50% to the total progress. + ProgressBar.setPercentage( + overallProgress, + 'Clustering in progress...' + ); + }; // call clustering function from hclust library - clust_results = clusterData({ data: data_merge, key: 'exps' }); + clust_results = clusterData({ + data: data_merge, + key: 'exps', + onProgress: onClusteringProgress, + }); // 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)); clust_results.order = sortOrder; // extract sort order from clust_results clusterReady = true; + ProgressBar.cleanUp(); } else if (doCluster && clusterReady) { // if clustering already done, no need to re-run sortOrder = clust_results.order; } From f47b79faf6af521784b851a511f3a4365809ed3a Mon Sep 17 00:00:00 2001 From: DongPing Lian Date: Wed, 17 Apr 2024 12:29:54 -0400 Subject: [PATCH 26/44] Clean up formatting for html files --- main/html/about.html | 78 +++++---- main/html/index.html | 381 +++++++++++++++++++++++++++---------------- 2 files changed, 292 insertions(+), 167 deletions(-) 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 a5735bf6..2bf81279 100644 --- a/main/html/index.html +++ b/main/html/index.html @@ -1,27 +1,41 @@ - - + + Web Genomics - - + - + - - + + - + @@ -30,7 +44,10 @@ - + @@ -38,54 +55,76 @@ -
    - -
    - +
    -
    - - +


    -
    +
    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 +

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


    -
    -
    +
    Customize Your Cohort:

    -
    -

    1) Select tumor type(s)

    +

    + 1) Select tumor type(s) +

    -

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

    -
    " + "" + "Hierarchical Clustering" + @@ -112,7 +116,7 @@ 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(); @@ -255,17 +259,7 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d ); return; } - if (doCluster && !clusterReady) { // do hierarchical clustering, if not already done (clusterReady)\ - ProgressBar.setPercentage(0, 'Beginning cluster'); - - // update the progress bar - const onClusteringProgress = (progress) => { - const overallProgress = progress * 100; // Since there are 2 phases, each contributes 50% to the total progress. - ProgressBar.setPercentage( - overallProgress, - 'Clustering in progress...' - ); - }; + if (doCluster && !clusterReady) { // do hierarchical clustering, if not already done (clusterReady) // call clustering function from hclust library clust_results = clusterData({ data: data_merge, @@ -278,7 +272,6 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d clust_results.order = sortOrder; // extract sort order from clust_results clusterReady = true; - ProgressBar.cleanUp(); } else if (doCluster && clusterReady) { // if clustering already done, no need to re-run sortOrder = clust_results.order; } diff --git a/main/js/plots/createViolinPlot.js b/main/js/plots/createViolinPlot.js index 1068ba3e..948c8e02 100644 --- a/main/js/plots/createViolinPlot.js +++ b/main/js/plots/createViolinPlot.js @@ -515,15 +515,19 @@ function standardDeviation(mean, values) let createViolinPartitionBox = async function(partitionDivId, geneQuery) { var div_box = d3.select('#'+partitionDivId); - div_box.append('text') - .style("font-size", "20px") + div_box + .append('text') + .style('font-size', '20px') + .style('padding-left', '10px') .text('Select variables to partition violin curves by:'); div_box.append('div') .attr('class','viewport') .attr("id", "partitionSelectViolinPlot") - .style('overflow-y', 'scroll') - .style('height', '300px') + // .style('overflow-y', 'scroll') + // .style('height', '460px') .style('width', '300px') + .style('text-align', 'left') + .style('padding-left', '20px') .append('div') .attr('class','body'); var selectedText = div_box.append('text'); @@ -539,8 +543,8 @@ let createViolinPartitionBox = async function(partitionDivId, geneQuery) if(cb.property('checked')){ choices.push(cb.property('value')); }; }); - if(choices.length > 0){ selectedText.text('Selected: ' + choices.join(', ')); } - else { selectedText.text('None selected'); }; + // if(choices.length > 0){ selectedText.text('Selected: ' + choices.join(', ')); } + // else { selectedText.text('None selected'); }; } // function to create a pair of checkbox and text @@ -564,7 +568,7 @@ let createViolinPartitionBox = async function(partitionDivId, geneQuery) .attr('value', data); label.append('text') - .text(data); + .text(' ' + data); } // data to input = clinical vars from query diff --git a/main/js/progressBar.js b/main/js/progressBar.js index 2c9f0b91..7cdcacbc 100644 --- a/main/js/progressBar.js +++ b/main/js/progressBar.js @@ -19,12 +19,14 @@ const ProgressBar = { this.percent = 0 else this.percent = Math.round(newPercent) + console.log(this.percent); this.rerender() }, cleanUp: function () { this.percent = 0 document.getElementById("progress-bar").innerText = ""; this.rerender() + console.log("Cleaned up") }, rerender: function () { const ele = document.querySelector(`#${this.id}`) From d8abc12b9e1b9adcadf68ea91bfabe36a78a5f6e Mon Sep 17 00:00:00 2001 From: DongPing Lian Date: Wed, 24 Apr 2024 12:12:25 -0400 Subject: [PATCH 29/44] Removed the large gap between content and footer. Section 2 and 3 are now only hidden when cancer types are being fetched. --- main/css/style.css | 32 +++++++++++++++++--------------- main/html/index.html | 33 +++++++++++---------------------- main/js/progressBar.js | 2 -- main/js/smartCache/main.js | 15 ++++++++++----- 4 files changed, 38 insertions(+), 44 deletions(-) diff --git a/main/css/style.css b/main/css/style.css index 3a3780b0..0dcf9558 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 { @@ -20,7 +21,7 @@ /* WebGen Title at top of app */ .PageTitle { - font-family: "Roboto", sans-serif; + font-family: 'Roboto', sans-serif; color: #4db6ac; text-align: center; font-size: 45px; @@ -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/html/index.html b/main/html/index.html index 2bf81279..c3aef654 100644 --- a/main/html/index.html +++ b/main/html/index.html @@ -90,7 +90,8 @@ style=" text-align: center; font-style: italic; - font-family: Georgia, 'Times New Roman', Times, serif; + font-family: Georgia, 'Times New Roman', Times, + serif; " > A tool for exploring data from The Cancer Genome Atlas @@ -135,11 +136,10 @@ onchange=" fillClinicalSelectBox(), displayNumberSamples(), - saveInLocalStorage(), - showOrHideGeneAndClinicalSelection() + saveInLocalStorage() " > - +
    @@ -193,7 +193,8 @@ style=" text-align: center; color: lightcoral; - font-family: Georgia, 'Times New Roman', Times, serif; + font-family: Georgia, 'Times New Roman', Times, + serif; " > Explore Your Cohort: @@ -249,7 +250,8 @@ style=" text-align: center; color: lightcoral; - font-family: Georgia, 'Times New Roman', Times, serif; + font-family: Georgia, 'Times New Roman', Times, + serif; " > Download Data: @@ -332,13 +334,13 @@ var instance = M.Tabs.init(elem, options);
    +