From 7b2bbe2c40efdd42715c4f337cb3959deeb431b2 Mon Sep 17 00:00:00 2001 From: BasLee Date: Thu, 10 Aug 2023 06:39:44 +0200 Subject: [PATCH] Add defaults for genomic evolution tab in patient view (#10309) * Add defaults for mutation heatmap and line chart checkboxes * Update text --------- Co-authored-by: Gaofei Zhao <15748980+dippindots@users.noreply.github.com> --- .../customization/portal.properties-Reference.md | 12 ++++++++++++ portal/src/main/webapp/config_service.jsp | 5 ++++- src/main/resources/portal.properties.EXAMPLE | 6 +++++- 3 files changed, 21 insertions(+), 2 deletions(-) diff --git a/docs/deployment/customization/portal.properties-Reference.md b/docs/deployment/customization/portal.properties-Reference.md index 19273b2d38a..5eca5c5988b 100644 --- a/docs/deployment/customization/portal.properties-Reference.md +++ b/docs/deployment/customization/portal.properties-Reference.md @@ -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 enable log scale and sequential mode by default, set this property to `true`: +``` +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. @@ -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`. diff --git a/portal/src/main/webapp/config_service.jsp b/portal/src/main/webapp/config_service.jsp index ab5bbf48c3e..5dc3ba8c9fe 100644 --- a/portal/src/main/webapp/config_service.jsp +++ b/portal/src/main/webapp/config_service.jsp @@ -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", @@ -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" }; diff --git a/src/main/resources/portal.properties.EXAMPLE b/src/main/resources/portal.properties.EXAMPLE index efae1b8c794..2d950289252 100644 --- a/src/main/resources/portal.properties.EXAMPLE +++ b/src/main/resources/portal.properties.EXAMPLE @@ -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:/ @@ -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= \ No newline at end of file +# download_group= + +# vaf.sequential_mode.default=false +# vaf.log_scale.default=false