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URL parameters
gene=<name>
Generates view for a gene. Example: https://proteinpaint.stjude.org/?genome=hg19&gene=ALK&dataset=clinvar
- Display a gene by given name. Value can be gene symbol or isoform accession, value is case-insensitive
- Requires “genome”
- Optionally, specify built-in datasets using parameter “dataset”:
- If more than 1, join by comma
- Dataset must be hosted on the PP server
- Value is case-insensitive
- Example to load the “Pediatric” dataset:
- When using datasets, highlight certain mutations matching with given name
- Effect: any groups of mutation showing a match with the given name will be shown as expanded. All the rest of groups are folded.
- This feature is only intended for point mutation AA change name. The provided name must exactly match with the content in the DB or VCF file
- Example:
- All types of custom track parameters can be used as well, as defined in the “block” section below.
block=1
Launches a genome browser. Example: https://proteinpaint.stjude.org/?block=on&genome=hg19&position=chr17:7568451-7591984&bigwigurl=UCSC_phyloP,http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP100way/hg19.100way.phyloP100way.bw
genome=<name>
Required. Provides reference genome name.
Optional. Specify genomic regions.
position=chr:start-stop
Coordinates are 0-based, example
- ?block=on&genome=hg19&position=chr1:1234-5678
Optionally, append a second region separated by semicolon. E.g. position=chr1:1234-5678;chr2:123-456 The second region is shown in a secondary panel that is scrolled independently from the first region.
regions=...
Value is multiple regions joined by comma. All regions are shown in one view and are scroll together.
- ?block=on&genome=hg19®ions=chr1:111-222,chr2:333-444
Experimental feature: there is a bug of incorrect genomic ruler rendering when providing multiple regions.
hlregion=chr:start-stop,...
Optional. Provide one or more regions to highlight. Each region is in the format of “chr:start-stop”. Do not use commas in start or stop positions. Join multiple regions by comma. There is a bug that it will highlight regions that are outside of view range.
Optional. There is no parameter called “tracks”, but many different parameters to provide different types of tracks.
bigwigfile=name,path/to/file.bw
bigwigurl=name,<URL>
To provide “bigWig” tracks. Learn how to generate a bigWig file
- Provide one or more bigwig tracks, each in the form of “name,path-or-url”, all joined by comma. When using file, the files are hosted in the directory of the ProteinPaint server
- Example
- ?bigwigfile=[name1],[path/to/file1.bw],[name2],[path/to/file2.bw],....
- ?bigwigurl=[name1],[url1],[name2],[url2]
- Note that this method won’t allow setting Y scale or other configurations
mds3bcffile=name,path/to/file.vcf.gz
Provide one bgzipped and tabix-indexed BCF tracks. Requires VCF 4.2 format. Each in the form of “name,path-or-url”, all joined by commas.
Example: https://proteinpaint.stjude.org/?genome=hg38&gene=kras&mds3bcffile=custom,hg38/clinvar.hg38.bcf.gz
mds3bcfurl=name,http://host/path/file.gz,http://host/path2/file.gz.csi
Provide one above-mentioned bcf file that is remotely hosted. The index file URL is optional and only required when it's hosted from a different place.
junctionfile=name,<path>
junctionurl=name,<URL>
Provide one or more junction tracks, see junction file format. Each in the form of “name,path-or-url”, all joined by commas.
URL format:
?junctionfile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],....
Note that this method won’t allow configuring the junction type.
mdsjunctionfile=name,<path>
“MDS junction” track is the v2.0 of the junction track, work-in-progress. This parameter will provide one or more tracks, the file of which are hosted on the ProteinPaint server.
URL format:
?mdsjunctionfile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],....
See mds=<dslabel>,<querykey> for method of launching a cohort junction track defined in an official GenomePaint dataset.
junctionmatrix=name,<path/to/file.gz>
Loads a junction-by-sample read count matrix file. First line of the file is the header, first 5 fields are required as below. Rest of the fields are samples. The track has been tested to work with as many as 10,000 samples.
#chr \t start \t stop \t strand \t type \t sample1 \t sample2 …
Each row is one junction.
- Start and stop positions are 0-based.
- Strand is always “+” for now.
- Type is either “known” or “novel”.
- Each sample field is the split read count. Blanks are allowed in place of 0.
The file must be sorted by coordinates, bgzipped, and tabix-index.
bedjfile=name,<path>
bedjurl=name,<URL>
Provide one or more JSON-BED tracks, see JSON-BED file format. Each in the form of “name,path-or-url”, all joined by comma.
bedjfilterbyname=<name>
Provide the ensembl IDs to filter JSON-BED tracks and/or NCBI IDs to filter RefGene tracks, separated by a space. URL format:
- bedjfilterbyname=[id1] [id2]...[idn] OR bedjfilterbyname=[id1]%20[id2]%20...[idn]
bamfile=name,<path>
bamurl=name,<path>
Provide one or more BAM tracks. Each in the form of “name,path-or-url”, all joined by comma. URL format:
- ?bamfile=[name1],[path/to/file1.bam],[name2],[path/to/file2.bam],....
aicheckfile=name,<path>
aicheck file format ?aicheckfile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],...
hictkfile=name,enzyme,<path>
hictkurl=name,enzyme,<URL>
Hi-C tracks to show as pyramid heatmap
hictknorm=STR
Can be used alongside hictkfile or hictkurl parameters. Value is comma-joined normalization strings e.g. VC, one string for each track.
arcfile=name,<path/to/file.gz>
ldfile=name,<path>
svcnvfpkmurl=name,<url>
svcnvfpkmfile=name,<path>
Submits a custom GenomePaint track, must have the “svcnv” file. FPKM and VCF files are optional.
URL format: ?svcnvfpkmurl=[track_name],svcnv,[URL to svcnv.gz file],fpkm,[URL to fpkm.gz file],vcf,[URL to vcf.gz file]
mds=<dslabel>,<querykey>
Launches an official GenomePaint track. URL format: ?mds=[dataset_label],[query_key] Example: https://proteinpaint.stjude.org/?block=on&genome=hg19&mds=Pediatric2,svcnv
An optional “sample” parameter could be added to launch Sample View, including the assay tracks available to that sample. Example: https://proteinpaint.stjude.org/?block=on&genome=hg19&mds=Pediatric2,svcnv&sample=SJWLM019896_D1-PAKUIT
The same method can be used to launch a cohort splice junction track defined in the same dataset. TODO add example here.
mdsjson=<path/to/file.json>
mdsjsonurl=<URL>
Launches a custom GenomePaint track using configurations defined in a JSON file. See JSON file specification.
mds3=<dslabel>
Launch a track with support for GDC API. Example: https://proteinpaint.stjude.org/?genome=hg38&gene=ENST00000407796&mds3=GDC
Optionally, the “token=” parameter can be used to supply a GDC token to access controlled data. Without it, it will only access open-access data.
tkjsonfile=<path/to/file.json>
Loads a set of tracks from a JSON file in the directory of the ProteinPaint server. The JSON file is an array mixture of track objects and facet tables. Please see our documentation on how to create the JSON.
mass=<stringified JSON>
mass-session-file=<path/to/file.json>
mass-session-url=<http://host/file.json>
mass-session-id=<sessionID>
study=<path/to/file.json>
Loads a study using the JSON file location.
URL format: ?study=path/to/mystudy.json Example: https://proteinpaint.stjude.org/?study=proteinpaint_demo/hg19/heatmap/heatmapDemo.json
On PP server, the corresponding file is /path/to/mystudy.json
View this tutorial on how to organize data into a study.
scatterplot=1
Launches a legacy scatter plot. This will be replaced by the sample scatterplot (below).
Requires one of the following keys mdsjson, mdsjsonurl or tsnejson.
tsnejson=<path/to/file.json>
Launches a custom samplescatterplot track using analysis data defined in JSON file. The JSON file should contain only data defined as analysisdata: { } in this document. See JSON file specification. Example: https://proteinpaint.stjude.org/?scatterplot=1&genome=hg38&tsnejson=proteinpaint_demo/hg38/mdstsne/file.json
singlecell=<path/to/file.json>
Launches single cell app using meta data and UMAP/tsne data defined in a JSON file. The JSON file may also contain expression data but at minimum “file” pointing to the UMAP data. See Single Cell Documentation.
mavbfile=<path/to/file>
mavburl=<path/to/file>
Provide the path to the text file. Requires the genome URL parameter. URL format: ?genome=[genomeName]&mavbfile=path/to/file.txt
gdcbamslice=1
Trigger the GDC BAM slicing user interface to view them as BAM tracks. Example: https://proteinpaint.stjude.org/?gdcbamslice=1
Add additional parameters to fill in fields:
appcard=<json file name || partial or complete card name>
**For internal use: Render a track or app sandbox from the app drawer with the json file name.
Acceptable URL formats for the JSON BED card:
?appcard=bedj OR ?appcard=JSON OR ?appcard=JSON BED
To open a specific example, use &example=<example name>
Open the Numeric Filter example in the JSON BED card:
?appcard=bed&example=Numeric Filter
Examples:
- BigWig: https://proteinpaint.stjude.org/?appcard=bigwig
- JSON BED: https://proteinpaint.stjude.org/?appcard=bedj
- Splice Junction: https://proteinpaint.stjude.org/?appcard=junction
- FusionEditor: https://proteinpaint.stjude.org/?appcard=fusioneditor
- Heatmap: https://proteinpaint.stjude.org/?appcard=study