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Add defaults for genomic evolution tab in patient view #10309

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Aug 10, 2023
Merged

Add defaults for genomic evolution tab in patient view #10309

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b408e9c
Add defaults for mutation heatmap and line chart checkboxes
BasLee Aug 2, 2023
952d17c
Update text
dippindots Aug 10, 2023
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12 changes: 12 additions & 0 deletions docs/deployment/customization/portal.properties-Reference.md
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,13 @@ Different samples of a patient may have been analyzed with different gene panels
skin.patientview.filter_genes_profiled_all_samples=
```

### Control default settings of the VAF line chart in the genomic evolution tab of patient view
If you want to enablelog scale and sequential mode by default, set this property to `true`:
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```
vaf.log_scale.default=true|false
vaf.sequential_mode.default=true|false
```

### Control unauthorized studies to be displayed on the home page

By default, on an authenticated portal the home page will only show studies for which the current user is authorized. By setting the _skin.home\_page.show\_unauthorized\_studies_ property to _true_ the home page will also show unauthorized studies. The unauthorized studies will appear greyed out and cannot be selected for downstream analysis in Results View or Study View.
Expand Down Expand Up @@ -436,6 +443,11 @@ oncoprint.oncokb.default=true|false
oncoprint.hotspots.default=true|false
```

If you want to enable oncoprint heatmap clustering by default, set this property to `true`:
```
oncoprint.clustered.default=true|false
```

**Automatic hiding of variants of unknown significance (VUS)**

By default, the selection box to hide VUS mutations is unchecked. If you want to automatically hide VUS, set this property to `true`. Default is `false`.
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5 changes: 4 additions & 1 deletion portal/src/main/webapp/config_service.jsp
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Expand Up @@ -38,6 +38,7 @@
"oncoprint.custom_driver_annotation.binary.default",
"oncoprint.oncokb.default",
"oncoprint.hotspots.default",
"oncoprint.clustered.default",
"genomenexus.url",
"genomenexus.url.grch38",
"google_analytics_profile_id",
Expand Down Expand Up @@ -147,7 +148,9 @@
"skin.patient_view.structural_variant_table.columns.show_on_init",
"comparison.categorical_na_values",
"study_download_url",
"skin.home_page.show_reference_genome"
"skin.home_page.show_reference_genome",
"vaf.sequential_mode.default",
"vaf.log_scale.default"
};


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6 changes: 5 additions & 1 deletion src/main/resources/portal.properties.EXAMPLE
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Expand Up @@ -316,6 +316,7 @@ oncoprint.oncokb.default=true
oncoprint.hotspots.default=true
# oncoprint.hide_vus.default=true
# oncoprint.clinical_tracks.config_json=classpath:/oncoprint-default-tracks.json
# oncoprint.clustered.default=true

# Custom gene sets
# querypage.setsofgenes.location=file:/<path>
Expand Down Expand Up @@ -435,4 +436,7 @@ persistence.cache_type=no-cache
# Allows download links within DataSets Tab (See Portal.Properties documentation for more info)
# study_download_url=

# download_group=
# download_group=

# vaf.sequential_mode.default=false
# vaf.log_scale.default=false
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