Docs:tutorials corrected

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: {

docs/visualization-community/data-manage/index.md

@@ -1,71 +1,61 @@
 ---
 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
  ``` 
  or 
  ```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). 

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.
+

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/).

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.

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

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

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**
 

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**
 

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

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

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

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**
 

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,

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":{