diff --git a/docs/visualization-community/basics/index.md b/docs/visualization-community/basics/index.md index b35d6c43..8838a0c2 100644 --- a/docs/visualization-community/basics/index.md +++ b/docs/visualization-community/basics/index.md @@ -2,19 +2,21 @@ title: Learning the Code Block Basics --- -To add code to the VisCom's editor, a +To add code to the VisCom's editor, a call must be used, which is written in JavaScript. To find more details about this software please see the [ProteinPaint Google Docs](https://docs.google.com/document/d/1JWKq3ScW62GISFGuJvAajXchcRenZ3HAvpaxILeGaw0/) for further detail. ```JS runproteinpaint() ``` -call must be used, which is written in JavaScript. To find more details about this software please see the [ProteinPaint Google Docs](https://docs.google.com/document/d/1JWKq3ScW62GISFGuJvAajXchcRenZ3HAvpaxILeGaw0/) for further detail. + !!!tip * ProteinPaint is case sensitive, but the URL key is case in-sensitive. -* Lollipop does not have a `file` or `url` parameter. +* Lollipop does not have a `file` or `url` key. * DataFacet Tables and 2DMAF are not supported in VisCom. * The code block has static parameters for many of the visualizations. See below an example: !!! +The below is the static code block that visualizations will share. `Holder` will be different in the ProteinPaint code examples so please be sure to use this one in VisCom. `Genome` will be dependent on the species that you are investigating. Further explanation of all attributes in ProteinPaint can be found [here](https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9) (page 3). + ```JS runproteinpaint({ host: "https://proteinpaint.stjude.org", @@ -27,7 +29,7 @@ runproteinpaint({ genome: hg38, ``` -`Holder` will be different in the ProteinPaint code examples so please be sure to use this one in VisCom. `Genome` will be dependent on the species that you are investigating. Further explanation of all attributes in ProteinPaint can be found [here](https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9) (page 3). +Then, each visualization contains a track or study view. These are comprised of different keys or elements describing that track. See the code block library in the left navbar for the specifics on each data type. Each track will require access to the data which by a url or path key. Mutation Landscape, splice junctions from a cohort, scatterplot, and single cell tracks accept JSON. ``` JS studyview: { diff --git a/docs/visualization-community/data-manage/index.md b/docs/visualization-community/data-manage/index.md index 19a899e1..af9cec59 100644 --- a/docs/visualization-community/data-manage/index.md +++ b/docs/visualization-community/data-manage/index.md @@ -1,7 +1,7 @@ --- title: Manage Your Data --- -In this section, you can learn which key to use based on where your data lives. +In this section, you will learn which key to use, based on where your data lives: ```JS url ``` @@ -9,63 +9,53 @@ In this section, you can learn which key to use based on where your data lives. ```JS file ``` -keys to run the -```JS -proteinpaint() -``` -command: -Follow the below tutorials depending on where your data lives: -Here you will want to follow the one highlighted below. +Follow the below tutorials depending on where your data lives: * if you have your data stored in DNAnexus, go [here](https://university.stjude.cloud/docs/genomics-platform/managing-data/upload-dnanexus/). * if you have your data stored on your local and want to upload to DNAnexus, go [here](https://university.stjude.cloud/docs/genomics-platform/managing-data/upload-local/). * if you have your data stored on the HPC and want to move them to DNAnexus, go [here](https://university.stjude.cloud/docs/genomics-platform/managing-data/upload-cluster/). !!!tip * The url key is case in-sensitive. -* Dropbox storage will not work since these are binary files. -* AW and DNAnexus are two examples that the `runproteinpaint()` can access. -* !!! +* Dropbox storage url keys will not work since these are binary files. +* Amazon (AWS) and DNAnexus are two examples that `runproteinpaint()` can access. +!!! -# Extending your DNAnexus download link +# Accessing DNAnexus from the command line (extend your file duration) First you will want to check if you have python installed. ```JS python --version ``` -Then, check if you have python3 installed. +Then, check if you have python3 installed ```JS python3 --version ``` -Install DNAnexus. +and install DNAnexus. ```JS pip3 install dxpy ``` -Open DNAnexus on the command line. +Open DNAnexus to ensure you can access it from the command line. ```JS dx ``` Get your token by logging into DNAnexus. Navigate to your profile icon. Select the API token in the top navbar. Select to generate the token. Then go to your terminal and enter: ```JS -dx login --token token_here +dx login --token add_token_here ``` - Type the below to see what project you are in. +Pick a project to enter and then type the below to see all files in that project. ```JS dx ls ``` - Type the below to go to a project. -```JS -dx cd -``` -Type the below to see the durations. +Type the below to see the durations ```JS dx make_download_url file_name.txt --help ``` -Type to set duration. +and then type to set duration. ```JS dx make_download_url file_name.txt --duration 100y ``` -Use this URL for VisCom so be sure to save this. +Use this URL for VisCom's url key, so be sure to save this. # Licensing If you wish to have your own license of ProteinPaint please follow this [guideline](https://www.stjude.org/research/why-st-jude/shared-resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html). \ No newline at end of file diff --git a/docs/visualization-community/datatypes/index.md b/docs/visualization-community/datatypes/index.md index 7e24938a..8c3e7e79 100644 --- a/docs/visualization-community/datatypes/index.md +++ b/docs/visualization-community/datatypes/index.md @@ -31,4 +31,5 @@ Below is a highlight of supported data types visualized by ProteinPaint and Geno | 2DMAF* | ![](./2dmaf-square.png) | | Data Facet Table* | ![](./tklist-square.png) | -* VisCom does not support 2DMAF or Data Facet Tables at this time, but ProteinPaint can. + *VisCom does not support 2DMAF or Data Facet Tables at this time. + diff --git a/docs/visualization-community/embed/index.md b/docs/visualization-community/embed/index.md index 8e07ff44..821f7802 100644 --- a/docs/visualization-community/embed/index.md +++ b/docs/visualization-community/embed/index.md @@ -13,7 +13,7 @@ In this part of the tutorial, one will learn how to [embed](https://stjudecloud. 4. Save the file with the .html suffix. 5. Drag and drop the .html file into the browser, open the saved .html file by double-clicking, or save within a website. - +For further details you can go [here](https://stjudecloud.github.io/docs/guides/proteinpaint/developers-guide/embedding-proteinpaint/). **Block Code Example** ```html @@ -51,4 +51,3 @@ In this part of the tutorial, one will learn how to [embed](https://stjudecloud. % ``` -For further details you can go [here](https://stjudecloud.github.io/docs/guides/proteinpaint/developers-guide/embedding-proteinpaint/). \ No newline at end of file diff --git a/docs/visualization-community/faq/index.md b/docs/visualization-community/faq/index.md index cad7fa57..f111b82f 100644 --- a/docs/visualization-community/faq/index.md +++ b/docs/visualization-community/faq/index.md @@ -4,10 +4,10 @@ title: Frequently Asked Questions KeyWord(s): VisCom (Visualization Community) **What is Visualization Community?** -* [Visualization Community](https://viz.stjude.cloud/) is a safe environment where you can explore public research visualizations, learn to use [ProteinPaint](https://proteinpaint.stjude.org/)/[GenomePaint](https://genomepaint.stjude.cloud/) to create your own visualizations, and even create visualizations that can be privately or publick accessed. +* [Visualization Community](https://viz.stjude.cloud/) is a safe environment where you can explore public research visualizations, learn to use [ProteinPaint](https://proteinpaint.stjude.org/)/[GenomePaint](https://genomepaint.stjude.cloud/) to create your own visualizations, and even create visualizations that can be privately or publicly accessed. **How does Visualization Community work?** -* VisCom is hosted in St. Jude's cloud enviornment where there is no outsource program or application to download. It only requires a computer and internet connection. It is completely free for non-profit/academic use. +* VisCom is hosted in St. Jude's cloud enviornment where there is no outsource program or application to download. It only requires a computer and internet connection and is completely free for non-profit/academic use. * You will ***not*** incur any costs except in the following situations: @@ -18,10 +18,10 @@ KeyWord(s): VisCom (Visualization Community) **Can I create my own visualizations?** * Yes, St. Jude internal users have access to create visuals now once they sign up for an account and are assigned a team. We are working on a new workflow so that you can create visuals without being on a team. -* As an external user, please contact support@stjude.cloud so that we can help you create an account. Then, you may follow our '**Getting Started**' chapter to follow step-by-step tutorials to begin creating your own visualizations within VisCom. +* As an external user, please contact support@stjude.cloud so that we can help you create an account. Then, you may follow our **Getting Started** chapter to follow step-by-step tutorials to begin creating your own visualizations within VisCom. **Can I share my visuals with others?** -* Yes, you may share your visualization(s) once created. Coming soon will be a sharing option within the Visualization Community platform. +* Yes, you may share your visualization(s) if our PI or team lead approves. We can enable a feature for you to share the direct link administratively if the visualization is still private. Coming soon will be a sharing option within the Visualization Community platform once the visualization is public. **Can I keep my visualizations private?** * Yes, we have an access control workflow where you can create visualizations which will remain private until you get approval from the team P.I. or Team Lead to to make it public. @@ -30,12 +30,26 @@ KeyWord(s): VisCom (Visualization Community) * Yes, you may use these sophisticated figures in your publications. We currently have published visualizations in over 11 prestigious journals including Nature, Cancer Discovery, Blood, and Cell Reports. **Do I have to upload my own PDF or what do I need to generate the interactive visualization?** -* You do not need to upload a PDF. You can either use ProteinPaint/GenomePaint as an internal user or follow our step-by-step tutorials to create a visual. -* While we have curated examples, custom content is allowed. +* You do not need to upload a PDF. You can either use ProteinPaint/GenomePaint to create a visual. While we have curated examples, custom content is allowed. **Can I access the data used to generate the visualizations?** * You can access the data within each Community on the 'Data tab' or by clicking the data source icon above each individual visualization. -**Can I build a Community?** -* Yes, you can curate a public or private Community to unify the visualizations and publications that are associated to propel the scientific community. +**What is a community?** +* A community is a platform within VisCom that allows teams (and/or multiple users) to share visualizations related to the same research. +* For example, Audacious Goals Initiative (AGI) - Retina provides a platform about retinal diseases that highlight studies and research across multiple labs. Not only are the labs studies showcased, but the data supporting the visualizations are accessible. + +* This platform can be empowering to share data, showcase visualizations, and propel discoveries. All communities have a logo and description that is tailored for that community’s initiative. + +* Please email support@stjude.cloud that you are interested in creating a community. Our admin team will reach out with the next steps. In general, we will want to set up an interview to understand your research and how you develop your data. Then, we will begin to roadmap the project so that we can get your branding (logo, description, and necessary data) completed. We will need access to your studies (publications, abstracts, etc) and then our team will work on how to get your visualizations in VisCom by providing one-on-one assistance, including a demonstration so that you can also develop visualizations on your own. + + +**What is a collection?** +* A collection is a setting where a user or team can group a set of visualizations to be viewed together. For example, a user may want to group a cohort of visualizations by data type or disease. + +* The collection will display as shown here. A collection can remain public, private, or private but with a direct link. + +* This can be a way to share visualizations in bulk by using our direct link setting, if all visualizations remain private. Or this is a way to share a collection of visualizations publicly for a direct purpose. + +* Please email support@stjude.cloud with the list of visualizations you want grouped into a collection, including a description for the landing page. If they are private, a direct link will be given to share with others or for individual use. diff --git a/docs/visualization-community/library/MA-Volcano/index.md b/docs/visualization-community/library/MA-Volcano/index.md index 10b08d00..efbcd0f0 100644 --- a/docs/visualization-community/library/MA-Volcano/index.md +++ b/docs/visualization-community/library/MA-Volcano/index.md @@ -7,7 +7,7 @@ These code block examples can be used to generate MA+Volcano plot by using a Big Use: Differential gene expression [ProteinPaint Google Docs](https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 4, 7, 9, 12, 14 and 17** ```JS @@ -38,8 +38,7 @@ runproteinpaint({ } }) ``` - -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 4, 7, 9, 12, 14 and 17** ```JS diff --git a/docs/visualization-community/library/ai-check/index.md b/docs/visualization-community/library/ai-check/index.md index 40e7819f..8d254ea2 100644 --- a/docs/visualization-community/library/ai-check/index.md +++ b/docs/visualization-community/library/ai-check/index.md @@ -8,7 +8,7 @@ Use: From tumor and germline DNA [ProteinPaint Google Docs](https://docs.google.com/document/d/1dZIOoLLbQE-kmZ31Ia_5cud30d9UeRodP4hRCSw3HII/) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 9, 14, 15** ```JS @@ -33,7 +33,7 @@ runproteinpaint({ ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 9, 14, 15** ```JS diff --git a/docs/visualization-community/library/arc/index.md b/docs/visualization-community/library/arc/index.md index c9a7247b..7bd34286 100644 --- a/docs/visualization-community/library/arc/index.md +++ b/docs/visualization-community/library/arc/index.md @@ -8,7 +8,7 @@ Use: View pair-wise chromatin interactions at a locus [ProteinPaint Google Docs](https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit#heading=h.8zct8j3cscak) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 9, 14 and 15** @@ -37,7 +37,7 @@ runproteinpaint({ ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 9, 14 and 15** diff --git a/docs/visualization-community/library/ase/index.md b/docs/visualization-community/library/ase/index.md index ec8683fc..eddf6fcf 100644 --- a/docs/visualization-community/library/ase/index.md +++ b/docs/visualization-community/library/ase/index.md @@ -8,7 +8,7 @@ Use: Allele-specific expression analysis [ProteinPaint Google Docs](https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit#heading=h.ly3x0hngycmz) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 7 and 9** @@ -43,7 +43,7 @@ runproteinpaint({ }) ``` -# Path to file EXAMPLE +# File Key Example **Be sure to update lines 7 and 9** diff --git a/docs/visualization-community/library/bam/index.md b/docs/visualization-community/library/bam/index.md index 5ee80dbf..753f173c 100644 --- a/docs/visualization-community/library/bam/index.md +++ b/docs/visualization-community/library/bam/index.md @@ -8,7 +8,7 @@ Use: sequence reads alignment [ProteinPaint Google Docs](https://docs.google.com/presentation/d/1oGI72Vooc25oAKir4DmarNDjDmUcigQk65FU8niSE_k/edit#slide=id.g8398dfdab9_0_0) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 9, 14 and 15** ```JS @@ -32,7 +32,7 @@ runproteinpaint({ }) ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 9, 14 and 15** ```JS diff --git a/docs/visualization-community/library/bigwig/index.md b/docs/visualization-community/library/bigwig/index.md index 1bd9c3c2..cab44c29 100644 --- a/docs/visualization-community/library/bigwig/index.md +++ b/docs/visualization-community/library/bigwig/index.md @@ -8,7 +8,7 @@ Use: Quantitative data at genomic postions [ProteinPaint Google Docs](https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 13, 14 and 15** ```JS @@ -32,7 +32,7 @@ runproteinpaint({ }) ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 13, 14 and 15** ```JS diff --git a/docs/visualization-community/library/bigwigstranded/index.md b/docs/visualization-community/library/bigwigstranded/index.md index dd471024..d26e90bd 100644 --- a/docs/visualization-community/library/bigwigstranded/index.md +++ b/docs/visualization-community/library/bigwigstranded/index.md @@ -7,7 +7,7 @@ These code block examples can be used to generate a figure using bigwig stranded Use: Quantitative data at genomic positions using forward and reverse strand reads [ProteinPaint Google Docs](https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.5m3g10g8lvol) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 9, 13, 16 and 19** ```JS @@ -38,7 +38,7 @@ runproteinpaint({ }) ``` -**Path to File EXAMPLE** +# File Key Example **Be sure to update lines 8, 9, 13, 16 and 19** ```JS diff --git a/docs/visualization-community/library/facet/index.md b/docs/visualization-community/library/facet/index.md index 2d518811..d2c13663 100644 --- a/docs/visualization-community/library/facet/index.md +++ b/docs/visualization-community/library/facet/index.md @@ -8,8 +8,8 @@ Use: [ProteinPaint Google Docs](https://docs.google.com/document/d/1e0JVdcf1yQDZst3j77Xeoj_hDN72B6XZ1bo_cAd2rss/edit#heading=h.pkybixxj4p6) -# URL Parameter EXAMPLE - +# URL Key Example +Coming soon: This currently is not supported with a url key at this time. **Be sure to update lines 7 and 9** ```JS @@ -25,7 +25,7 @@ runproteinpaint({ }) ``` -# Path to file EXAMPLE +# File Key Example **Be sure to update lines 7 and 9** diff --git a/docs/visualization-community/library/fusion/index.md b/docs/visualization-community/library/fusion/index.md index b1f131c7..48eeab14 100644 --- a/docs/visualization-community/library/fusion/index.md +++ b/docs/visualization-community/library/fusion/index.md @@ -10,6 +10,7 @@ https://pecan.stjude.cloud/static/hg19/fusioneditor/cicero.output const host = 'https://proteinpaint.stjude.org' const rawtext = 'copy output file here' +**Viscom does not support this visualization type at this time.** ```JS runproteinpaint({ host: host, diff --git a/docs/visualization-community/library/heatmap/index.md b/docs/visualization-community/library/heatmap/index.md index 6978e124..c3db8877 100644 --- a/docs/visualization-community/library/heatmap/index.md +++ b/docs/visualization-community/library/heatmap/index.md @@ -8,7 +8,7 @@ For additional learning of each element or key please go to the heatmap [Protein **This code block below is for snv files. If you have SV or fusion transcript, CNV, ITD, Intragenic deletion/in-frame, Truncation, then we cannot support these at this time from the url key.** -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update line 6, 9, and 11. Update lines 14-16 if you have JSON** ``` JS @@ -33,7 +33,7 @@ runproteinpaint({ ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update line 6, 9, and 11. Update lines 14-16 if you have JSON** ```JS @@ -56,10 +56,12 @@ runproteinpaint({ } }) ``` -Adding a mutation set for more than one data type (snv, copy number, fusion, etc) is expert-level customization. Currently, VisCom only allows the `snvindel_url` key, but if you have other data types, then please reach out so that we can support this for you. These would display as *Mutation Types* as seen below: +Adding a mutation set for more than one data type (snv, copy number, fusion, etc) is expert-level customization. Currently, VisCom only allows the `snvindel_url` key. We are working to add these keys which would display as *Mutation Types* as seen below: + ![](./mutation_type.png) Formats for the file types are listed below and the hyperlinks are found at the ProteinPaint mutation landscape track. + ![](./format.png) Once we can support this, it can be coded as: @@ -101,7 +103,7 @@ To view an example of the JSON file format: Furthermore, you can convert an excel sheet to JSON. There are many ways to do this, but we recommend [BeautifyTools](https://beautifytools.com/excel-to-json-converter.php) and to debug use [https://jsonlint.com/](https://jsonlint.com/). # Further Customization -If you want to add ProteinPaint or GenomePaint viewers to the genes, please use the below, but the files used must be specific to render correctly. If you have trouble, please reach out. +If you want to add ProteinPaint or GenomePaint viewers to the genes, please see below, but the files used must be specific to render correctly. If you have trouble, please reach out. ```JS "heatmapJSON":{ diff --git a/docs/visualization-community/library/hic/index.md b/docs/visualization-community/library/hic/index.md index b287a229..ccceffc0 100644 --- a/docs/visualization-community/library/hic/index.md +++ b/docs/visualization-community/library/hic/index.md @@ -8,7 +8,7 @@ These code block examples can be used to generate a heatmap as seen in [VisCom]( Use: View chromatin interactions at a locus [ProteinPaint Google Docs](https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 9, 14, 15 and 19** ``` JS @@ -36,7 +36,7 @@ runproteinpaint({ }) ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 9, 14, 15 and 19** ``` JS diff --git a/docs/visualization-community/library/json-bed/index.md b/docs/visualization-community/library/json-bed/index.md index b4d8488e..be9e2290 100644 --- a/docs/visualization-community/library/json-bed/index.md +++ b/docs/visualization-community/library/json-bed/index.md @@ -9,7 +9,7 @@ Use: Genomic feature alignment [ProteinPaint Google Docs](https://docs.google.com/document/d/1GP81rer7YEb0RpIej2XXfx-k7SCAL1Od9At_oczf06A/) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 12, 13, 16** ```JS @@ -34,7 +34,7 @@ runproteinpaint({ }); ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 12, 13, 16** ```JS diff --git a/docs/visualization-community/library/pgv/index.md b/docs/visualization-community/library/pgv/index.md index 3ffc92a2..a6656afe 100644 --- a/docs/visualization-community/library/pgv/index.md +++ b/docs/visualization-community/library/pgv/index.md @@ -7,7 +7,7 @@ These code block examples can be used to generate a profile gene value (pvg) as Use: Profiling results & gene-level values [ProteinPaint Google Docs](https://docs.google.com/document/d/1yrRpDUZWSRGuCa0snGwRuo721WRHgdYTX7GWIsZ_fSY/) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 10, 14, 16, 18, 22, 23, 24 and 25** @@ -41,7 +41,7 @@ runproteinpaint({ }] }); ``` -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 10, 14, 16, 18, 22, 23, 24 and 25** diff --git a/docs/visualization-community/library/rna-splice-junction/index.md b/docs/visualization-community/library/rna-splice-junction/index.md index f5e6105c..f303793d 100644 --- a/docs/visualization-community/library/rna-splice-junction/index.md +++ b/docs/visualization-community/library/rna-splice-junction/index.md @@ -10,7 +10,7 @@ Use: See splice junctions of RNA [ProteinPaint Google Docs](https://docs.google.com/document/d/1PFva3Mn-U4VPNW0vHHC-CSnYBeotRnqbhCMQPmyLQG4/edit) -# URL Parameter EXAMPLE +# URL Key Example **Be sure to update lines 8, 13, 14, 17, 18, 21, 22** ```JS @@ -43,7 +43,7 @@ runproteinpaint({ }) ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 13, 14, 17, 18, 21, 22** ```JS diff --git a/docs/visualization-community/library/singlecell/index.md b/docs/visualization-community/library/singlecell/index.md index 3645da4a..deae9e97 100644 --- a/docs/visualization-community/library/singlecell/index.md +++ b/docs/visualization-community/library/singlecell/index.md @@ -8,23 +8,11 @@ These code block examples can be used to generate a Single-Cell figure by using Use: Single Cell omics viewer [ProteinPaint Google Docs](https://docs.google.com/document/d/1YVxw2aPru6bAlTzUfE9GAQAvzbiBiqJiBR1X-g5ZBLI/edit) -# URL Parameter EXAMPLE - -**Be sure to update lines 6 and 7** -```JS -runproteinpaint({ - host:'https://proteinpaint.stjude.org', - holder:document.getElementById('aaa'), - noheader:1, - singlecell:{ - genome:'galGal5', - jsonUrl:'enter link here' - }, -}) -``` +# URL Key Example +Coming soon: This currently is not supported with a url key at this time. -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 6 and 7** ```JS diff --git a/docs/visualization-community/library/splice-junctions-cohort/index.md b/docs/visualization-community/library/splice-junctions-cohort/index.md index 328903fd..2539f0f6 100644 --- a/docs/visualization-community/library/splice-junctions-cohort/index.md +++ b/docs/visualization-community/library/splice-junctions-cohort/index.md @@ -10,30 +10,10 @@ Use: See splice junctions of a cohort [ProteinPaint Google Docs](https://docs.google.com/document/d/1e0JVdcf1yQDZst3j77Xeoj_hDN72B6XZ1bo_cAd2rss/edit#heading=h.s58v64uwsl45) -# URL Parameter EXAMPLE +# URL Key Example +Coming soon: This currently is not supported with a url key at this time. -**Be sure to update lines 8, 13 and 14** -```JS -runproteinpaint({ - host: "https://proteinpaint.stjude.org", - holder: visualizationContainer[0], - parseurl: true, - block: true, - nobox: 1, - noheader: 1, - genome: "hg19", - nativetracks: "RefGene", - tracks: [ - { - "type": "junction", - "url": "enter link here", - "name": "name of track" - } - ] -}); -``` - -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 8, 13 and 14** ```JS diff --git a/docs/visualization-community/library/tnse/index.md b/docs/visualization-community/library/tnse/index.md index 6b2bf2c3..f96e71be 100644 --- a/docs/visualization-community/library/tnse/index.md +++ b/docs/visualization-community/library/tnse/index.md @@ -8,7 +8,10 @@ Use: 2D scatterplot of samples & metadata [ProteinPaint Google Docs](https://docs.google.com/document/d/1XHi_WqVdarUNbc_ESMEBp2l-zwhnGcIfiBWA5n2omZQ/) -# Path to file EXAMPLE +# URL Key Example +Coming soon: This currently is not supported with a url key at this time. + +# File key Example **Be sure to update lines 8, 9, 14, 15** ```JS diff --git a/docs/visualization-community/library/vcf/index.md b/docs/visualization-community/library/vcf/index.md index 1323ced5..58bbd665 100644 --- a/docs/visualization-community/library/vcf/index.md +++ b/docs/visualization-community/library/vcf/index.md @@ -8,7 +8,7 @@ Use: Explore coding and non-coding variants in cancer [ProteinPaint Google Docs](https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit) -# URL Parameter EXAMPLE +# URL Key EXAMPLE **Be sure to update lines 7, 8, 13, 14 and 15** ``` JS @@ -33,7 +33,7 @@ runproteinpaint({ ``` -# Path to File EXAMPLE +# File Key Example **Be sure to update lines 7, 8, 13 and 14** ```JS diff --git a/docs/visualization-community/overview/index.md b/docs/visualization-community/overview/index.md index c6df4b3b..651c15f3 100644 --- a/docs/visualization-community/overview/index.md +++ b/docs/visualization-community/overview/index.md @@ -5,27 +5,25 @@ title: Getting Started Each section in **Getting Started** will have an overview of what you will learn and then give step-by step instructions. We encourage you to follow the sections in order if this is your first time exploring the help guides. **What you will learn:** -* How to sign in to Visualization Community (VisCom). -* How to build a template. -* How to manage your data. -* How to use the code block library for the VisCom editor. -* How to create a collection or community. -* How to enable a visualization for the public or share a private visualization. -* How to embed your visualizations. +* How to [sign in](https://university.stjude.cloud/docs/visualization-community/sign-in/) to Visualization Community (VisCom). +* How to [build a template](https://university.stjude.cloud/docs/visualization-community/template/). +* How to [manage your data](https://university.stjude.cloud/docs/visualization-community/data-manage/). +* How to use the [code block library](https://university.stjude.cloud/docs/visualization-community/basics/) for the VisCom editor. +* How to c[reate a collection or community](https://university.stjude.cloud/docs/visualization-community/col_com/). +* How to enable to share a visualization for the [public or a private visualization](https://university.stjude.cloud/docs/visualization-community/public_private/). +* How to [embed](https://university.stjude.cloud/docs/visualization-community/embed/) your visualizations. -Examples of curated visualizations are found in [VisCom](https://viz.stjude.cloud/st-jude-cloud-demo/collection/proteinpaint-and-genomepaint-examples~7). +Examples of curated visualizations can be found in [VisCom](https://viz.stjude.cloud/st-jude-cloud-demo/collection/proteinpaint-and-genomepaint-examples~7). -For additional learning about ProteinPaint please go to the [ProteinPaint Google Docs](https://docs.google.com/document/d/1JWKq3ScW62GISFGuJvAajXchcRenZ3HAvpaxILeGaw0/). +For additional learning about [ProteinPaint](https://proteinpaint.stjude.org/) please go to the [ProteinPaint Google Docs](https://docs.google.com/document/d/1JWKq3ScW62GISFGuJvAajXchcRenZ3HAvpaxILeGaw0/). -If you have any questions, please reach out to [support@stjude.cloud](support@stjude.cloud). - -If you need to cite St. Jude Cloud, please follow this [link](https://university.stjude.cloud/docs/citing-stjude-cloud). +If you have any questions, please reach out to [support@stjude.cloud](support@stjude.cloud) or if you need to cite St. Jude Cloud, please follow this [link](https://university.stjude.cloud/docs/citing-stjude-cloud).

Coming Soon!

- Video series describing how to generate visuals per data type

+ Video series covering various topics for an optimal user experience.

diff --git a/docs/visualization-community/sign-in/index.md b/docs/visualization-community/sign-in/index.md index c3541b85..2aa341b3 100644 --- a/docs/visualization-community/sign-in/index.md +++ b/docs/visualization-community/sign-in/index.md @@ -1,11 +1,11 @@ --- title: How to Sign-In --- -In this section, you will learn how to sign-up and sign-in so that you can create visualizations within an account. Once you sign-up, you will need to be associated to a team to create a visualization, see below on how to proceed. You can go to [Visualization Community](https://viz.stjude.cloud/) and immediately begin exploring without being logged in. +In this section, you will learn how to sign-up and/or sign-in so that you can create visualizations within an account. Once you sign-up, you will need to be associated to a team to create a visualization, see below on how to proceed. In the meantime, you can go to [Visualization Community](https://viz.stjude.cloud/) and immediately begin exploring without being logged in. **New User** -To sign up for a new account, you must first go to [viz.stjude.cloud/signin](viz.stjude.cloud/signin). account authentication, be sure to select to remember your credentials so that you do not have to enter it again each time. It will then refresh to the home page of Visualization Community. When you are done, contact [support@stjude.cloud](support@stjude.cloud) to be added to a team. +To sign up for a new account, you must first go to [viz.stjude.cloud/signin](viz.stjude.cloud/signin). Once you complete the account authentication, be sure to select to remember your credentials so that you do not have to enter it again each time. It will then refresh to the home page. When you are done, contact [support@stjude.cloud](support@stjude.cloud) to be added to a team. **Existing User** diff --git a/docs/visualization-community/template/codeblock.png b/docs/visualization-community/template/codeblock.png new file mode 100644 index 00000000..a939cc6a Binary files /dev/null and b/docs/visualization-community/template/codeblock.png differ diff --git a/docs/visualization-community/template/index.md b/docs/visualization-community/template/index.md index d79f9df2..b62ab38f 100644 --- a/docs/visualization-community/template/index.md +++ b/docs/visualization-community/template/index.md @@ -2,15 +2,17 @@ title: How to Build a Template --- -Each visualization made in your team will display in a list view. The visualization will remain private until your PI or team lead approves it in written form to [support@stjude.cloud](support@stjude.cloud). See the Public vs. Private section for more details. +Each visualization made in your team will display in a list view. The visualization will remain private until your PI or team lead approves it in written form to [support@stjude.cloud](support@stjude.cloud). See the **Public vs. Private** chapter for more details. ## Open a New Template When you are logged in, have navigated to teams as aforementioned in the previous section, then select a team from the list, and go to the **Visualizations** tab. + ![](./team_list.png) All the visualizations made by that team will populate. Scroll to the bottom of the list and select **Create Visualization**. + ![](./create_button.png) This will populate an empty template. You may select a thumbnail image to represent your visualization and fill in the following fields: @@ -24,12 +26,13 @@ This will populate an empty template. You may select a thumbnail image to repres ## Learn the Code Block Basics -If you need to learn more about the code block basics go [here]. +If you need to learn more about the code block basics go [here](https://university.stjude.cloud/docs/visualization-community/basics/). ## Build Your Code Now that you have briefly learned about how the code block works, let's select a code block for the visualization you want to create. Go to the **Code Block Library** on the left and select which data type you will be using to create your visualization. -![](./visualize_list.png) + +![](./codeblock.png) Next, let's learn which example you need to copy and paste into the VisCom editor so that ProteinPaint can access your data and render your visualization. Each example either has a @@ -40,7 +43,7 @@ or a ```JS url ``` -parameter. Some visualizations may have more than 1 ```url``` key; if this happens, the library example will explain what to do. +key. Some visualizations may have more than 1 ```url``` key; if this happens, the library example will explain what to do. Below describes how to get the `file` path or `url`. # Manage your Data @@ -58,11 +61,12 @@ After you select the code block, depending on where the data lives, and update t To render the visualization, click ‘Update Visualization’ within VisCom. ![](./finalize_vis.png) You should get a success banner. -![](.success.png) + +![](./success.png) Next, click the Go Back button at the top of the visualization template. Then, click the title of the visualization to render it. -If you have any errors due to file formatting or within the ```runproteinpaint()```, the error will be validated and shown. Therefore, go back to your list of visualizations and click the icon to edit. +If you have any errors due to file formatting or code block, the error will be validated and shown after you open your visualization. Therefore, go back to your list of visualizations and click the icon to edit. ![](./view_vis.png) diff --git a/src/config/docs.yaml b/src/config/docs.yaml index 4bc7069d..1760a299 100644 --- a/src/config/docs.yaml +++ b/src/config/docs.yaml @@ -131,8 +131,6 @@ domains: path: /docs/visualization-community/col_com/ - title: "Public vs Private Visualizations" path: /docs/visualization-community/public_private/ - - title: "Video Tutorials" - path: /docs/visualization-community/videos/ - title: "Embedding" path: /docs/visualization-community/embed/ - title: "Code Block Library"