warnings

docs/visualization-community/basics/index.md

@@ -24,7 +24,7 @@ runproteinpaint({
 
 Further explanation of all attributes in ProteinPaint can be found [here](https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9) (page 3).
 
-!!!Tip
+!!!tip
 For the traditional code editor to work, it must have true JSON where each attribute is closed within quotes.
 !!!
 

docs/visualization-community/editors/index.md

@@ -101,15 +101,15 @@ This is helpful when a team is proactively curating their visualizations and dat
 
 !!!tip
 Visualizations will change statuses based on where it is in the approval process:
-Draft - blue
-Waiting for review - yellow
-Needs Review - red
-Revisions requested - red
-Approved - green
+Draft - blue; 
+Waiting for review - yellow; 
+Needs Review - red; 
+Revisions requested - red; 
+Approved - green; 
 !!!
 
 # Export
-Export a SVG of the visualization.
+Export a SVG of the visualization to use for publications or other related material.
 
 # Docs
 This will take you to the visualization community help guides. 

docs/visualization-community/index.md

@@ -15,7 +15,7 @@ Once you find the visualization you need within VisCom, you can easily re-create
 
 *If you want to use the new VisEditor with a curated example data found in VisCom, then just be sure to copy/paste the file or url key hyperlink to re-create it. Add the hyperlink to the URL field that populates for that track or app. 
 
-![](./explore.png)
+![](./Explore.png)
 
 ## Purpose
 * You can explore shared visualizations by searching or filtering by institution, data type, lab, author, PubMedID, and even by diagnosis. 

docs/visualization-community/library/MA-Volcano/index.md

@@ -9,9 +9,8 @@ Use: The MA plot contrasts the magnitude of expression (M) on the x axis against
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit)
 
 
-### Supported by the Traditional Code Editor only
-!!!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.
+!!!warning
+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. Supported by the Traditional Code Editor only.
 !!!
 
 # URL Parameter EXAMPLE

docs/visualization-community/library/ai-check/index.md

@@ -10,7 +10,7 @@ Use: Displays the allelic imbalance of the heterozygous SNP markers in a tumor g
 
 # URL Key Example
 
-!!!tip
+!!!warning
 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 <gz> files they must also have the <tbi> file associated. What happens is that the ProteinPaint looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
 !!!
@@ -35,7 +35,7 @@ In order to render <gz> files they must also have the <tbi> file associated. Wha
 
 # File Key Example
 
-!!!tip
+!!!warning
 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.
 !!!

docs/visualization-community/library/arc/index.md

@@ -7,13 +7,13 @@ These code block examples can be used to generate an arc figure as seen in [VisC
 Use: Used to display chromatin capture data by focusing on the frequency of links between distant genomic regions.
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit#heading=h.8zct8j3cscak)
 
-!!!tip
+!!!warning
 <mode_arc> must be true with <mode_hm> set to false for the arc to render. If <mode_arc> is false, then it behaves like a Hi-C where the pyramid is up. Additional configs can be found in the UI of the visualization. <percentile_max> is for the resolution of the Hi-C plot. <gz> and <tbi> files are not accepted for Hi-C at this time. 
 !!!
 
 # URL Key Example
 
-!!!Tip
+!!!warning
 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 <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.>
 !!!
@@ -43,7 +43,7 @@ In order to render <gz> files they must also have the <tbi> file associated. Wha
 
 # File Key Example
 
-!!!Tip
+!!!warning
 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.
 !!!

docs/visualization-community/library/bam/index.md

@@ -11,7 +11,7 @@ Use: Visualizes the aligned reads and assists in understanding depth and quality
 
 # URL Key Example
 
-!!!tip
+!!!warning
 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 ProteinPaint looks for the <abi> file and cannot parse the <bam> so we must give it an alternate path to the <bai> file.>
 !!!
@@ -36,7 +36,7 @@ In order to render <bam> files they must also have the <bai> file associated. Wh
 
 # File Key Example
 
-!!!tip
+!!!warning
 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.
 !!!

docs/visualization-community/library/bigwig/index.md

@@ -10,7 +10,7 @@ Use: This format shows the depths of reads in RNA seq, ChIP seq, or genomic sequ
 
 # URL Key Example
 
-!!!tip
+!!!warning
 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.
 !!!
 
@@ -34,7 +34,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 
 # File Key Example
 
-!!!tip
+!!!warning
 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.
 !!!

docs/visualization-community/library/bigwigstranded/index.md

@@ -9,7 +9,7 @@ Use:  RNA-seq coverage data as a pair of bigWig tracks, with forward strand on t
 
 # URL Key Example
 
-!!!tip
+!!!warning
 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.
 !!!
 
@@ -40,7 +40,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 
 # File Key Example
 
-!!!tip
+!!!warning
 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.
 !!!

docs/visualization-community/library/expression-rank/index.md

@@ -10,7 +10,7 @@ Use: RNA-seq coverage data as a pair of bigWig tracks, with forward strand on to
 
 # URL Parameter EXAMPLE
 
-!!!tip
+!!!warning
 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. The <sample> parameter must be unique to the file otherwise it will **not** render. 
 !!!
 
@@ -36,7 +36,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 
 # Path to file EXAMPLE
 
-!!!tip
+!!!warning
 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.
 !!!

docs/visualization-community/library/heatmap/index.md

@@ -19,7 +19,7 @@ Truncation [Format](https://drive.google.com/open?id=1P1g-Y8r30pSKfan1BhYZcsUtSk
 
 # URL Parameter EXAMPLE
 
-!!!tip
+!!!warning
 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. Each data type has its own url key. 
 !!!
 

docs/visualization-community/library/hic/index.md

@@ -13,7 +13,7 @@ Not currently supported in the VisEditor. No URL key enabled.
 
 # File Key Example
 
-!!!tip
+!!!warning
 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. <percentile_max> is for the resolution of the Hi-C plot. <pyramidup> must be 1 to be upward or 0 for downward. <enzyme> is the restriction enzyme used to cut. <gz> and <tbi> files are not accepted for Hi-C at this time. 
 !!!
 

docs/visualization-community/library/json-bed/index.md

@@ -11,7 +11,7 @@ Use: This customizable bed format shows defined genomic regions identified by Ch
 
 # URL Key Example
 
-!!!tip
+!!!warning
 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.
 !!!
 

docs/visualization-community/library/lollipop/index.md

@@ -9,7 +9,7 @@ Use: Used for displaying the frequency and type of mutation for a given gene on
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1D78jKVaQrWBhAjnfmCqj0Cirf6s-CdcbfPkuZQMT8Co/edit#heading=h.tyjcwt)
 
 
-!!!tip
+!!!warning
 This is a track and will be uplifted into the new VisEditor easy view soon.
 !!!
 

docs/visualization-community/library/pgv/index.md

@@ -8,7 +8,7 @@ Use: Used to display gene. expression results from RNA seq across a cohort of sa
 
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1yrRpDUZWSRGuCa0snGwRuo721WRHgdYTX7GWIsZ_fSY/)
 
-!!!tip
+!!!warning
 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. The <file> keys can be switched with <url> keys. Legendimg is optional.
 !!!
 

docs/visualization-community/library/rna-splice-junction/index.md

@@ -9,7 +9,7 @@ These code block examples can be used to generate a RNA splice junction from a c
 Use: This visualization displays the number of mapped junction reads precisely along with a gene model and will include alternative splicing and isoforms if available.
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1PFva3Mn-U4VPNW0vHHC-CSnYBeotRnqbhCMQPmyLQG4/edit)
 
-!!!Tip
+!!!warning
 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 <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.>
 !!!

docs/visualization-community/library/vcf/index.md

@@ -7,7 +7,7 @@ These code block examples can be used to generate a figure using vcf data as see
 Use: This track localizes the variant data on reference genomes and can render frequency data for cohorts.
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit)
 
-!!!tip
+!!!warning
 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 <gz> files they must also have the <tbi> file associated. What happens is that the ProteinPaint looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
 !!!

docs/visualization-community/tracks_apps/index.md

@@ -6,11 +6,7 @@ Visualization Community supports GenomePaint and ProteinPaint tracks and apps.
 
 **Genome Browser tracks**: this versatile app allows direct comparison of multi-omic data aligned along a common genome. Built-in reference data is also available for select genomes (some regions may not be in view). Users can customize an array of multiple samples from multiple data types. These all render in our easy view editor. 
 
-**Apps**: This collection of diverse visualizations provides intuitive data exploration. Each app has a precise use case example. Built-in reference data is also available for select genomes (some regions may not be in view). These all render in our code editor. 
-
-A list for each is below:
-**Genome Viewer (App)**
-Tracks:
+**Tracks:**
 GenomePaint,
 JSON Bed,
 Hi-C
@@ -20,17 +16,19 @@ Arc Track,
 BAM,
 BigWig,
 Allelic Imbalance,
-Expression Rank
+Expression Rank,
+VCF
 
 
-**Apps:**
-Fusion Editor,
+**Apps**: This collection of diverse visualizations provides intuitive data exploration. Each app has a precise use case example. Built-in reference data is also available for select genomes (some regions may not be in view). These all render in our code editor. 
+
 Mutation Landscape,
 Scatterplot,
 MA+ Volcano plot,
 Single Cell,
 Lollipop*,
+Profile Gene Value*,
 Track list and Data facet Table*
 
-* Listed as Apps due to the VisEditor functionality. These are seen as Tracks in the original [ProteinPaint](https://proteinpaint.stjude.org/) site. 
+  *Listed as Apps due to the VisEditor functionality. These are seen as Tracks in the original [ProteinPaint](https://proteinpaint.stjude.org/) site. 
 

src/config/docs.yaml

@@ -176,8 +176,6 @@ domains:
                 path: /docs/visualization-community/library/pgv/
               - title: "Track List and Facet Table"
                 path: /docs/visualization-community/library/facet/
-              - title: "Fusion Editor"
-                path: /docs/visualization-community/library/fusion/
               - title: "t-SNE"
                 path: /docs/visualization-community/library/tsne/
           - title: "ProteinPaint"