Skip to content

Commit

Permalink
doc changes
Browse files Browse the repository at this point in the history
  • Loading branch information
@Ssandor13
Ssandor13 committed Mar 19, 2022
1 parent 3183518 commit a6c8da0
Show file tree
Hide file tree
Showing 24 changed files with 548 additions and 797 deletions.
49 changes: 25 additions & 24 deletions docs/visualization-community/basics/index.md
View file
@@ -1,36 +1,33 @@
---
title: Learning the Code Block Basics
---
Our new visualization editor allows you to prompt tracks for genome views without having to build any code.
Our new visualization editor allows you to build visualizations using our new editor interface. The interface prompts certain fields that are required to generate the visualization so you can spend more time exploring and creating visualizations and less time coding.

!!!Apps vs tracks
All tracks can be accessed via our easy editor, but all apps must be rendered by the traditional code editor.
!!!

To add code to VisCom's editor, a <runproteinpaint> call must be used. To find more details about this software, please see the [ProteinPaint Google Docs](https://docs.google.com/document/d/1JWKq3ScW62GISFGuJvAajXchcRenZ3HAvpaxILeGaw0/) for further detail.

Example data for all tracks can be found by downloading [this](https://pecan.stjude.cloud/static/pp-support/pp.demo.tgz) tarball (~30m).
For a description about each field, see our [How to use our Editor](https://university.stjude.cloud/docs/visualization-community/editors/) section. There are 2 ProteinPaint tracks that must render from our Traditional Code Editor: [Lollipop](https://university.stjude.cloud/docs/visualization-community/library/lollipop/) and [Track List and Data Facet](https://university.stjude.cloud/docs/visualization-community/library/facet/). The remaining Apps also will use the Traditional Code Editor at this time. Check out the other code blocks in the left navbar. Lastly, the tracks use a track object where the apps have defined objects and thus why apps and tracks are not combined together.

!!!tip
* ProteinPaint is case sensitive, but the URL key is case in-sensitive.
* Lollipop does not have a `file` or `url` key.
* 2DMAF is not supported in VisCom.
!!!
Example data for all tracks and apps can be found by downloading [this](https://pecan.stjude.cloud/static/pp-support/pp.demo.tgz) tarball (~30m). This data is used to prefill our VisEditor.

Below is the static code block that most visualizations will share. `Holder` will be different in the ProteinPaint code examples so please be sure to use <visualizationContainer[0]> in VisCom. Additionally, `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).
Below are the static attributes that run in the background and not seen in the code block or interface:

```JS
runproteinpaint({
host: "https://proteinpaint.stjude.org",
holder: visualizationContainer[0],
host: "https://proteinpaint.stjude.org", //this server is public facing
holder: visualizationContainer[0], //ProteinPaint.stjude.org examples use a different holder
parseurl: true,
block: true,
block: true, //only used for tracks, not apps
nobox: 1,
noheader: 1,
nativetracks: "RefGene",
genome: hg38,
//Below are two attributes that show in the interface.
nativetracks: "RefGene", // is a toggle in the UI
genome: hg38, // is a dropdown in the UI, but needs to be in the traditional code block
```
Further explanation of all attributes in ProteinPaint can be found [here](https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9) (page 3).
!!!Important
For the traditional code editor to work, it must have true JSON where each attribute is closed within quotes.
!!!
ProteinPaint has a GenomeViwer where multiple tracks can be run together or a user can run individual Apps.
**A list of each is below:**
**Genome Viewer (App)**
Expand All @@ -49,12 +46,16 @@ Lollipop,
Track list and Data facet Table
**APPS:**
Fusion Editor
Mutation heatmap
Scatterplot
MA+ Volcano plot
Fusion Editor,
Mutation heatmap,
Scatterplot,
MA+ Volcano plot,
Single Cell
See the code block library in the left navbar for the specifics on each track or app. They either require a <url> or <file> key to access your data. The tracks use a track object where the apps have defined objects and thus why apps and tracks are not combined together.
See the code block library in the left navbar for the specifics on each track or app. They either require a <url> (and <indexURL>) or <file> key to access your data. Briefly, <url> is to an open source data storage like DNAnexus or AWS. In order to render <gz> files they must also have the <tbi> file associated. What happens is that the <runproteinpaint()> looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
5 changes: 3 additions & 2 deletions docs/visualization-community/data-manage/index.md
View file
Expand Up @@ -4,10 +4,10 @@ title: Manage Your Data
In this section, you will learn how and where to find your data so that you can use our visualization editors.

!!!tip
* The url key is case in-sensitive.
* The <url> key is case in-sensitive.
* Dropbox storage url keys will not work since these are binary files.
* Amazon (AWS) and DNAnexus are two examples that `runproteinpaint()` can access.
* The <file> key is only for internal St. Jude users to access the HPC.
* The <file> key is only for internal St. Jude users to access the HPC within the <tp> directory.
!!!

Follow the below tutorials if you want to upload data to DNAnexus.
Expand Down Expand Up @@ -64,6 +64,7 @@ cd /research/rgs01/resgen/legacy/gb_customTracks/tp
```

Here, you can make a new directory to store your data.

!!!Important
The data must be on the proteinpaint.stjude.org server and not ppr1, otherwise your visualizations have to be viewed by VPN.
!!!
Expand Down
7 changes: 4 additions & 3 deletions docs/visualization-community/editors/index.md
View file
Expand Up @@ -50,12 +50,13 @@ Here is where you can add metadata about the visualization and is required for o
**Visibility** - enabled once the PI/Team lead approves so that it can remain private (by default) or set to public which publishes to Visualization Community.

# Code Editor
This it the traditional code editor for more advanced developers that may want to explore running the proteinpaint() argument. We do have select curated code blocks in our library section. If you choose to code your own visualization with this editor, it must meet proteinpaint's requirements which can be accessed by XXXXXX.
Once it is approved through the review process, if it is toggled to public on the info section of the visualization editor, it will report to support@stjude.cloud to be accepted. We must review the code to ensure there are no security issues.
This it the traditional code editor for more advanced developers that may want to explore running the proteinpaint() argument. We do have select curated code blocks in our library section. If you choose to code your own visualization with this editor, it must meet proteinpaint's requirements which can be accessed by going to each code block example and clicking the ProteinPaint documentation hyperlink.

Once the visualization is approved through the review process, if it is toggled to public on the info section of the visualization editor, it will report to support@stjude.cloud to be accepted. We must review the code to ensure there are no security issues.

# Save and reload
The visualization editor will save all changes in memory and then once you save it will create a template to access. If you do not save, it will not save the latest changes to your visualization in your account.
note

# Send for Review
This is our review process where you can send a visualization for review, with a custom message, to the PI/Team lead for the team you associate the visualization to so that they can review the visualization and decide whether to request for revisions or approve. At this time, the visualization is read-only. If the PI/Team lead asks for revisions, then the visualization will show their message and be editable. Throughout the process, the status of the visualization will change accordingly.

Expand Down
3 changes: 1 addition & 2 deletions docs/visualization-community/index.md
View file
Expand Up @@ -10,7 +10,6 @@ With over 71 publicly curated visualizations, an average of 1k views (greatest >

Once you find the visualization you need within VisCom, you can easily re-create it by copying the curated code block displayed for a visualization, by viewing our [library](https://university.stjude.cloud/docs/visualization-community/basics) of curated code blocks, or explore our new visualization editor with curated examples in your account.

![](./viz_home.gif)

## Purpose
* You can explore shared visualizations by searching or filtering by institution, data type, lab, author, PubMedID, and even by diagnosis.
Expand Down Expand Up @@ -40,5 +39,5 @@ If you wish to have your own license of ProteinPaint please follow this [guideli
<p align="center">
</a> Updates to ProteinPaint and GenomePaint guides</p>
<p align="center">
</a> More visualizations will be accessed view our new editor</a></p>
</a> More visualizations will be accessed via our new editor</a></p>

80 changes: 23 additions & 57 deletions docs/visualization-community/library/MA-Volcano/index.md
View file
Expand Up @@ -7,64 +7,30 @@ 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 Key Example

**Be sure to update lines 4, 7, 9, 12, 14 and 17**
```JS
runproteinpaint({
host: "https://proteinpaint.stjude.org",
holder: visualizationContainer[0],
genome: "hg19",
noheader: 1,
mavolcanoplot: {
genome: "hg19",
noheader: 1,
url: "enter hyperlink here",
tracks: [
{
name: "name of track",
strand1: {
url: "name/filetopath/sense.bw"
},
strand2: {
url: "name/filetopath/antisense.bw",
normalize: {
dividefactor: -1
}
},
type: "bigwigstranded"
}
]
}
})
```
# File Key Example
Supported by the Traditional Code Editor only.
You can switch out the <file> key with <url> key.

**Be sure to update lines 4, 7, 9, 12, 14 and 17**
```JS
runproteinpaint({
host: "https://proteinpaint.stjude.org",
holder: visualizationContainer[0],
genome: "hg19",
noheader: 1,
mavolcanoplot: {
genome: "hg19",
noheader: 1,
file: "enter file path here",
tracks: [
{
name: "name of track",
strand1: {
url: "name/filetopath/sense.bw"
},
strand2: {
url: "name/filetopath/antisense.bw",
normalize: {
dividefactor: -1
}
},
type: "bigwigstranded"
}
]
}
})
{
"genome":"hg19",
"mavolcanoplot": {
"url": "https://pecan.stjude.cloud/static/pp-support/example.files/DIPG_H33K27MvsWT_noACVR_adj.txt",
"tracks": [
{
"name": "Demo RNA-seq coverage",
"strand1": {
"file": "proteinpaint_demo/hg19/mavb/mavb_demo_sense.bw"
},
"strand2": {
"file": "proteinpaint_demo/hg19/mavb/mavb_demo_antisense.bw",
"normalize": {
"dividefactor": -1
}
},
"type": "bigwigstranded"
}
]
}
}
54 changes: 3 additions & 51 deletions docs/visualization-community/library/ase/index.md
View file
Expand Up @@ -8,55 +8,7 @@ Use: Allele-specific expression analysis
[ProteinPaint Google Docs](https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit#heading=h.ly3x0hngycmz)


# URL Key Example
!!!URGENT
Not currently supported in the VisEditor
!!!

**Be sure to update lines 7 and 9**

```JS
runproteinpaint({
holder:document.getElementById('visualization_container'),
host:'https://proteinpaint.stjude.org',
parseurl:true,
nobox:1,
block:1,
noheader:1,
position:'chr5:1252462-1297568',
genome:'hg38',
nativetracks:'refgene',
tracks:[
{
type:'ase',
name:'Demo ASE',
url:'enter link here',
indexUrl: 'enter link here',
hetsnp_minbaf:0.1,
hetsnp_maxbaf:0.8,
samplename:'sample name',
url: 'proteinpaint_demo/hg38/ase/sample12.bam',
indexUrl: 'enter link here',
rnabamtotalreads: 155650314,
checkrnabam:{
hetsnp_minbaf:.2,
hetsnp_maxbaf:.8
}
}
]
})
```

# File Key Example

**Be sure to update lines 7 and 9**

```JS
runproteinpaint({
"host": "https://proteinpaint.stjude.org/",
"holder": visualizationContainer[0],
"block": 1,
"nobox": 1,
"noheader": 1,
"genome": "hg19",
"nativetracks":"refgene",
"tkjsonfile": "proteinpaint_demo/hg19/tklist/tracks.json"
})
```
79 changes: 40 additions & 39 deletions docs/visualization-community/library/bam/index.md
View file
Expand Up @@ -8,51 +8,52 @@ Use: sequence reads alignment
[ProteinPaint Google Docs](https://docs.google.com/presentation/d/1oGI72Vooc25oAKir4DmarNDjDmUcigQk65FU8niSE_k/edit#slide=id.g8398dfdab9_0_0)



# URL Key Example

**Be sure to update lines 8, 9, 14 and 15**
!!!Tip
If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
In order to render <bam> files they must also have the <bai> file associated. What happens is that the <runproteinpaint()> looks for the <abi> file and cannot parse the <bam> so we must give it an alternate path to the <bai> file.>
!!!

**Be sure to update lines 1, 3, 8, 9, and 10**
```JS
runproteinpaint({
host:'https://proteinpaint.stjude.org',
holder: visualizationContainer[0],
parseurl:true,
block: true,
nobox:1,
noheader:1,
genome:'hg19',
position:'chr4:55589707-55589907',
nativetracks:'RefGene',
tracks:[   
{
type:'bam',
url:'enter .bam link here',
indexURL: 'enter .bai link here',
name:'name of track',
}
]
})
{
"genome": "hg38",
"nativetracks": "RefGene",
"position": "chr4:55589607-55590007",
"block": true,
"tracks": [
{
"type": "bam",
"name": "Track name",
"url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/QGf0F8zB4GYBzPQKg27BvkPgqgk90yqyKfz67gVy\/kit.exon8.del.bam",
"indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/gp8VX25X9YkKvKQqkjvfjPgz834zX51V0x6j7zF0\/kit.exon8.del.bam.bai"
}
]
}
```

# File Key Example

**Be sure to update lines 8, 9, 14 and 15**
!!!Tip
If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
!!!

**Be sure to update lines 1, 3, 8, and 9**
```JS
runproteinpaint({
host:'https://proteinpaint.stjude.org',
holder: visualizationContainer[0],
parseurl:true,
block: true,
nobox:1,
noheader:1,
genome:'hg19',
position:'chr4:55589707-55589907',
nativetracks:'RefGene',
tracks:[   
{
type:'bam',
file:'paste name/path_to_file/.bam',
name:'name of track',
}
]
})
{
"genome": "hg38",
"nativetracks": "RefGene",
"position": "chr4:55589607-55590007",
"block": true,
"tracks": [
{
"type": "bam",
"name": "Track name",
"file": "proteinpaint_demo\/hg19\/bam\/kit.exon8.del.bam"
}
]
}
```

0 comments on commit a6c8da0

Please sign in to comment.