From e8a6bca3e86d3c13718ac1a97cd997180bc47f8b Mon Sep 17 00:00:00 2001 From: "Abeshouse, Adam A./Sloan Kettering Institute" Date: Wed, 4 Dec 2019 16:03:02 -0500 Subject: [PATCH] oncoprint - allow adding gaps to string-valued clinical tracks Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute --- ...linical_track_element_chrome_1600x1000.png | Bin 0 -> 56696 bytes .../specs/core/oncoprint.screenshot.spec.js | 51 ++++++++++++------ package.json | 2 +- .../tools/oncoprinter/Oncoprinter.tsx | 6 +-- src/shared/components/oncoprint/DeltaUtils.ts | 5 +- .../oncoprint/ResultsViewOncoprint.tsx | 6 +-- .../oncoprint/controls/OncoprintControls.tsx | 1 + yarn.lock | 8 +-- 8 files changed, 51 insertions(+), 28 deletions(-) create mode 100644 end-to-end-test/remote/screenshots/reference/coadread_tcga_pub_with_column_gaps_inserted_based_on_clinical_track_element_chrome_1600x1000.png diff --git 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this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()/0.7); + this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()/0.7); }, onClickZoomOut:()=>{ - this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()*0.7); + this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()*0.7); } }; } diff --git a/src/shared/components/oncoprint/DeltaUtils.ts b/src/shared/components/oncoprint/DeltaUtils.ts index 0d61c645bcc..d63fe3f7ec5 100644 --- a/src/shared/components/oncoprint/DeltaUtils.ts +++ b/src/shared/components/oncoprint/DeltaUtils.ts @@ -785,7 +785,7 @@ function transitionClinicalTrack( rule_set_params.legend_label = nextSpec.label; rule_set_params.exclude_from_legend = !nextProps.showClinicalTrackLegends; rule_set_params.na_legend_label = nextSpec.na_legend_label; - const clinicalTrackParams = { + const clinicalTrackParams:UserTrackSpec = { rule_set_params, data: nextSpec.data, data_id_key: "uid", @@ -804,7 +804,8 @@ function transitionClinicalTrack( init_sort_direction: 0 as 0, target_group: CLINICAL_TRACK_GROUP_INDEX, onSortDirectionChange: nextProps.onTrackSortDirectionChange, - custom_track_options: nextSpec.custom_options + custom_track_options: nextSpec.custom_options, + track_can_show_gaps: nextSpec.datatype === "string" }; trackSpecKeyToTrackId[nextSpec.key] = oncoprint.addTracks([clinicalTrackParams])[0]; } else if (nextSpec && prevSpec) { diff --git a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx index 34fe7e9de2a..8f4e8fbf2fc 100644 --- a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx +++ b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx @@ -659,13 +659,13 @@ export default class ResultsViewOncoprint extends React.Component{ - this.oncoprint.setHorzZoom(z); + this.oncoprint.setHorzZoomCentered(z); }, onClickZoomIn:()=>{ - this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()/0.7); + this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()/0.7); }, onClickZoomOut:()=>{ - this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()*0.7); + this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()*0.7); } }; } diff --git a/src/shared/components/oncoprint/controls/OncoprintControls.tsx b/src/shared/components/oncoprint/controls/OncoprintControls.tsx index 68e1114b74a..5ee0f9705c0 100644 --- a/src/shared/components/oncoprint/controls/OncoprintControls.tsx +++ b/src/shared/components/oncoprint/controls/OncoprintControls.tsx @@ -1279,6 +1279,7 @@ export default class OncoprintControls extends React.Component< onClick={this.toggleShowMinimap} >