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index b80cb8a1..d355fd18 100644 --- a/dist/common/forms.js +++ b/dist/common/forms.js @@ -10,7 +10,7 @@ import { GeneUtils } from './GeneUtils'; * List of ids for parameter form elements * Reuse this ids and activate the `useSession` option for form elements to have the same selectedIndex between different views */ -export class ParameterFormIds { +class ParameterFormIds { } ParameterFormIds.DATA_SOURCE = 'data_source'; ParameterFormIds.GENE_SYMBOL = 'gene_symbol'; @@ -28,6 +28,7 @@ ParameterFormIds.COMPARISON_VALUE = 'comparison_value'; ParameterFormIds.COMPARISON_CN = 'comparison_cn'; ParameterFormIds.SCORE_FORCE_DATASET_SIZE = 'maxDirectFilterRows'; ParameterFormIds.COLOR_CODING = 'form_color_coding'; +export { ParameterFormIds }; export const COMPARISON_OPERATORS = [ { name: '< less than', value: '<', data: '<' }, { name: '<= less equal', value: '<=', data: '<=' }, diff --git a/dist/common/forms.js.map b/dist/common/forms.js.map index 12f15b0a..bca7fb4c 100644 --- a/dist/common/forms.js.map +++ b/dist/common/forms.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/scss/abstracts/_variables.scss b/dist/scss/abstracts/_variables.scss new file mode 100644 index 00000000..e69de29b diff --git a/dist/scss/components/_expression_vs_copynumber.scss b/dist/scss/components/_expression_vs_copynumber.scss new file mode 100644 index 00000000..72a68787 --- /dev/null +++ b/dist/scss/components/_expression_vs_copynumber.scss @@ -0,0 +1,66 @@ +.expressionVsCopyNumber, .coExpression { + + .title { + font-weight: 500; + } + + .axis path, + .axis line { + fill: none; + stroke-width: 1; + stroke: $core_color_almost_black; + shape-rendering: crispEdges; + } + + .mark { + fill: $core_color_almost_black; + fill-opacity: 0.8; + cursor: pointer; + + &.clicked { + stroke: $select-data-color; + fill-opacity: 1; + stroke-width: 2; + } + + &.disabled { + fill-opacity: 0.1; + } + + &:active, + &:focus, + &:hover { + stroke: $hover-data-color; + fill-opacity: 1; + stroke-width: 2; + } + } + + .tdp-legend { + padding: 1em; + display: flex; + flex: 1 1 100%; + width: 100%; + + flex-direction: row; + flex-wrap: wrap; + justify-content: flex-start; + + > div { + flex: 0 0 auto; + margin: 0 0.5em; + max-width: 15em; + overflow-x: hidden; + text-overflow: ellipsis; + } + + &:empty { + display: none; + } + } + + .spearmancoeff { + text-align: center; + } + +} diff --git a/dist/scss/components/_legend.scss b/dist/scss/components/_legend.scss new file mode 100644 index 00000000..ef166382 --- /dev/null +++ b/dist/scss/components/_legend.scss @@ -0,0 +1,15 @@ +.tdp-legend { + div { + cursor: pointer; + + span:first-child { + display: inline-block; + width: 10px; + height: 10px; + } + + &.disabled { + opacity: 0.5; + } + } +} diff --git a/dist/scss/components/_onco_print.scss b/dist/scss/components/_onco_print.scss new file mode 100644 index 00000000..cdb7f55d --- /dev/null +++ b/dist/scss/components/_onco_print.scss @@ -0,0 +1,392 @@ +$oncoprint_cell_height: 25px !default; +$oncoprint_cell_width: 7px !default; +$oncoprint_cell_padding: 2px !default; +$oncoprint_cell_mutation: 8px !default; + +$oncoprint_cnv_amplified: '2' !default; +$oncoprint_cnv_amplified_color: #efb3bc !default; +$oncoprint_cnv_amplified_border: transparent !default; + +$oncoprint_cnv_deep_deletion: '-2' !default; +$oncoprint_cnv_deep_deletion_color: #92c5de !default; +$oncoprint_cnv_deep_deletion_border: transparent !default; + +$oncoprint_cnv_normal: '0' !default; +$oncoprint_cnv_normal_color: #dcdcdc !default; +$oncoprint_cnv_normal_border: transparent !default; + +$oncoprint_cnv_unknown: 'NaN' !default; +$oncoprint_cnv_unknown_color: #FCFCFC !default; +$oncoprint_cnv_unknown_border: #dcdcdc !default; + +$oncoprint_mut_mutated: 'true' !default; +$oncoprint_mut_mutated_color: #1BA64E !default; +$oncoprint_mut_mutated_border: transparent !default; +$oncoprint_mut_not_mutated: 'false' !default; +$oncoprint_mut_not_mutated_color: #aaa !default; +$oncoprint_mut_not_mutated_border: transparent !default; +$oncoprint_mut_unknown: 'NaN' !default; +$oncoprint_mut_unknown_color: transparent !default; +$oncoprint_mut_unknown_border: #999 !default; + +$oncoprint_label_width: 10em !default; + +div.parameters .oncoPrintScale { + display: inline-flex; + + &[data-scale^='sss'] > button:first-of-type { + cursor: not-allowed; + } + &[data-scale^='s'] { + button:last-of-type { + cursor: pointer; + } + } + &[data-scale^='s'] > div { + div:nth-of-type(3) { + background: none; + } + button:last-of-type { + cursor: not-allowed; + } + } + &[data-scale^='ss'] > div { + div:nth-of-type(2) { + background: none; + } + } + &[data-scale^='sss'] > div { + div:nth-of-type(1) { + background: none; + } + } + > div { + display: flex; + align-items: flex-end; + + > div { + border: 1px solid #aaa; + width: 5px; + margin: 1px; + background: #dcdcdc; + + &:first-of-type { + height: 33%; + } + &:nth-of-type(2) { + height: 66%; + } + &:last-of-type { + height: 100%; + } + } + } + button { + border: none; + background: none; + } + > button:last-of-type { + cursor: not-allowed; + } +} + +.oncoPrint { + display: flex; + flex-direction: column; + overflow-x: hidden; + + .legend { + border-top: 1px solid $core_border; + width: 100%; + order: 1; // place at the bottom of gene list + + display: flex; + + list-style: none; + padding: 0; + margin: 0; + margin-top: 10px; + padding-top: 20px; + + ul { + margin: 0 40px 0 0; + padding: 0; + } + + .title { + font-weight: 500; + } + + li { + display: flex; + align-items: center; + margin-bottom: 3px; + + &::before { + display: inline-block; + content: ''; + border: 1px solid transparent; + width: 10px; + height: 25px; + margin-right: 5px; + } + + &[data-mut]::before { + width: 8px; + height: 8px; + } + } + + li[data-cnv='#{$oncoprint_cnv_amplified}']::before { + background-color: $oncoprint_cnv_amplified_color; + border-color: $oncoprint_cnv_amplified_border; + } + + li[data-cnv='#{$oncoprint_cnv_normal}']::before { + background-color: $oncoprint_cnv_normal_color; + border-color: $oncoprint_cnv_normal_border; + } + + li[data-cnv='#{$oncoprint_cnv_deep_deletion}']::before { + background-color: $oncoprint_cnv_deep_deletion_color; + border-color: $oncoprint_cnv_deep_deletion_border; + } + + li[data-cnv='#{$oncoprint_cnv_unknown}']::before { + background-color: $oncoprint_cnv_unknown_color; + border-color: $oncoprint_cnv_unknown_border; + } + + li[data-mut='#{$oncoprint_mut_mutated}']::before { + background-color: $oncoprint_mut_mutated_color; + border-color: $oncoprint_mut_mutated_border; + } + + li[data-mut='#{$oncoprint_mut_not_mutated}']::before { + background-color: $oncoprint_mut_not_mutated_color; + border-color: $oncoprint_mut_not_mutated_border; + } + + li[data-mut='#{$oncoprint_mut_unknown}']::before { + background-color: $oncoprint_mut_unknown_color; + border-color: $oncoprint_mut_unknown_border; + } + } + + > .alert-info { + order: 2; // place at the bottom of gene list + } + + .geneTableWrapper { + margin-left: $oncoprint_label_width; + overflow-x: auto; + overflow-y: hidden; + padding-bottom: 10px; // space for gene tooltip on hover + } + + td, th { + margin: 0; + white-space: nowrap; + } + + th.geneLabel { + cursor: move; + position: absolute; + left: 0; + top: auto; + color: $core_colour_text; + width: $oncoprint_label_width; + text-align: left; + + .ensg { + display: block; + font-size: 12px; + color: #ccc; + } + + .alterationFreq { + float: right; + margin-right: 5px; + margin-top: 10px; + } + } + + .gene { + margin-top: 10px; + display: flex; + align-items: center; + height: $oncoprint_cell_height + $oncoprint_cell_padding; + + &:first-child { + margin-top: 0; + } + + &.ui-sortable-helper th.geneLabel { + left: -$oncoprint_label_width; + } + + .cell { + position: relative; + display: flex; + align-items: center; + justify-content: center; + margin: 2px; + width: $oncoprint_cell_width + $oncoprint_cell_padding; + height: 100%; + border: 1px solid transparent; + + &.selected { + border-color: $select-color !important; + } + + .mut { + width: 80%; + border: 1px solid transparent; + height: $oncoprint_cell_mutation; + } + + &:after{ + display: block; + visibility: hidden; + position: absolute; + bottom: -35px; + left: -50%; + opacity: 0; + content: attr(data-title); + height: auto; + padding: 5px 8px; + z-index: 999; + color: #fff; + text-decoration: none; + text-align: center; + background: rgba(0,0,0,1); + border-radius: 3px; + pointer-events: none; + transition: all 0.2s ease-in-out; + white-space: nowrap; + } + + &:before { + position: absolute; + visibility: hidden; + width: 0; + height: 0; + bottom: -8px; + left: -10%; + opacity: 0; + content: ""; + border-style: solid; + border-width: 0 5px 8.7px 5px; + border-color: transparent transparent rgba(0,0,0,1) transparent; + pointer-events: none; + transition: all 0.2s ease-in-out; + } + + &:active:after, + &:active:before, + &:focus:after, + &:focus:before, + &:hover:after, + &:hover:before{ + visibility: visible; + opacity: 1; + } + + + &[data-cnv='#{$oncoprint_cnv_amplified}'] { + background-color: $oncoprint_cnv_amplified_color; + border-color: $oncoprint_cnv_amplified_border; + } + + &[data-cnv='#{$oncoprint_cnv_normal}'] { + background-color: $oncoprint_cnv_normal_color; + border-color: $oncoprint_cnv_normal_border; + } + + &[data-cnv='#{$oncoprint_cnv_deep_deletion}'] { + background-color: $oncoprint_cnv_deep_deletion_color; + border-color: $oncoprint_cnv_deep_deletion_border; + } + + &[data-cnv='#{$oncoprint_cnv_unknown}'] { + background-color: $oncoprint_cnv_unknown_color; + border-color: $oncoprint_cnv_unknown_border; + } + + &[data-mut='#{$oncoprint_mut_mutated}'] div { + background-color: $oncoprint_mut_mutated_color; + border-color: $oncoprint_mut_mutated_border; + } + + &[data-mut='#{$oncoprint_mut_not_mutated}'] div { + background-color: $oncoprint_mut_not_mutated_color; + border-color: $oncoprint_mut_not_mutated_border; + } + + &[data-mut='#{$oncoprint_mut_unknown}'] div { + background-color: $oncoprint_mut_unknown_color; + border-color: $oncoprint_mut_unknown_border; + } + } + + // last row --> tooltip on top + &:last-child:not(:first-child) .cell { + &:after { + top: -35px; + bottom: auto; + } + + &:before { + bottom: auto; + top: -8px; + border-width: 8.7px 5px 0 5px; + border-color: rgba(0,0,0,1) transparent transparent transparent; + } + } + + // only row --> tooltip to right + &:last-child:first-child .cell { + &:after { + bottom: -3px; + left: 15px; + } + + &:before { + z-index: 1; + bottom: 30%; + left: 7px; + border-width: 5px 8.7px 5px 0; + border-color: transparent rgba(0,0,0,1) transparent transparent; + } + } + } + &[data-scale^='s'] { + .cell { + margin-left: 1px; + margin-right: 1px; + width: 6px; + + .mut { + width: 100%; + } + } + } + &[data-scale^='ss'] { + .cell { + margin-left: 0; + margin-right: 0; + width: 5px; + } + } + + &[data-scale^='sss'] { + .cell { + border: none; + width: 3px; + + &.selected { + border: 1px solid $select-color; + } + } + } +} diff --git a/dist/scss/components/_species.scss b/dist/scss/components/_species.scss new file mode 100644 index 00000000..131f2154 --- /dev/null +++ b/dist/scss/components/_species.scss @@ -0,0 +1,14 @@ +.species-group { + .mouse-icon:before { + content: ''; + display: block; + height: 0.85em; + background: no-repeat center/50px url('../../assets/previews/mouse-icon.png'); + opacity: 0.1; + transition: opacity 0.2s ease-in-out; + } + + & label:hover .mouse-icon:before, &.active .mouse-icon:before { + opacity: 1; + } +} diff --git a/dist/scss/components/_startMenu.scss b/dist/scss/components/_startMenu.scss new file mode 100644 index 00000000..5fd659aa --- /dev/null +++ b/dist/scss/components/_startMenu.scss @@ -0,0 +1,136 @@ +.startMenu { + + .speciesSelector { + .body { + .species-wrapper { + display: flex; + padding-bottom: 15px; + border-bottom: 1px solid $core_border; + margin-bottom: 5px; + } + + .entry-points-wrapper { + margin-top: 15px; + } + + .species-group { + position: relative; + + &.active:before { + position: absolute; + width: 0; + height: 0; + bottom: -22%; + left: 25%; + content: ""; + border-style: solid; + border-width: 0 13px 13.7px 13px; + border-color: transparent transparent $header-menu-bg-color transparent; + pointer-events: none; + } + + &.active:after { + position: absolute; + width: 0; + height: 0; + bottom: -23%; + left: 26%; + content: ""; + border-style: solid; + border-width: 0 12px 12.7px 12px; + border-color: transparent transparent #fff transparent; + pointer-events: none; + } + } + + label[for^="speciesSelector"] { + cursor: pointer; + margin-right: 1em; + padding: 0.6em .25em .6em; + border: solid .2em $core_border; + border-radius: .5em; + position: relative; + color: $core_colour_selected; + + transition: background-color, color ease 0.2s; + + &:after { + display: block; + visibility: hidden; + position: absolute; + bottom: -66%; + left: 4%; + opacity: 0; + content: attr(data-title); + text-transform: capitalize; + height: auto; + padding: 5px 8px; + z-index: 999; + color: #fff; + text-decoration: none; + text-align: center; + background: rgba(0, 0, 0, 1); + border-radius: 3px; + pointer-events: none; + transition: all 0.2s ease-in-out; + white-space: nowrap; + } + + &:before { + position: absolute; + visibility: hidden; + width: 0; + height: 0; + bottom: -16%; + left: 42%; + opacity: 0; + content: ""; + border-style: solid; + border-width: 0 5px 8.7px 5px; + border-color: transparent transparent rgba(0, 0, 0, 1) transparent; + pointer-events: none; + transition: all 0.2s ease-in-out; + } + + &:active:after, + &:active:before, + &:focus:after, + &:focus:before, + &:hover:after, + &:hover:before { + visibility: visible; + opacity: 1; + } + } + + label:active, + label:focus, + label:hover, + input[type=radio]:checked + label { + color: $core_colour_text; + border-color: $core_colour_text; + } + + input[type=radio] { + display: none; + } + + .startMenuSearch { + margin-top: 10px; + display: flex; + justify-content: space-between; + + form { + width: 80%; + } + } + } + } + + .speciesSelector > header > h1 > label:before { + @extend .fas; + content: fa-content($fa-var-database); + width: 1.8em; + text-align: center; + } +} diff --git a/dist/scss/main.scss b/dist/scss/main.scss new file mode 100644 index 00000000..b6fff12a --- /dev/null +++ b/dist/scss/main.scss @@ -0,0 +1,13 @@ +@import "./abstracts/variables"; + +@import "./overrides/select2"; +@import "./overrides/idtype_color"; + +// styles for views +@import "./components/onco_print"; +@import "./components/expression_vs_copynumber"; +@import "./components/species"; +@import "./components/startMenu"; +@import "./components/legend"; + +@import "./menu/DatasetCard.scss"; \ No newline at end of file diff --git a/dist/scss/menu/DatasetCard.scss b/dist/scss/menu/DatasetCard.scss new file mode 100644 index 00000000..e16c1442 --- /dev/null +++ b/dist/scss/menu/DatasetCard.scss @@ -0,0 +1,9 @@ +.mouse-icon { + &::before { + content: ""; + display: block; + height: 0.85rem; + background: no-repeat center/20px + url("~tdp_publicdb/dist/assets/mouse-icon.png"); + } + } diff --git a/dist/scss/overrides/_idtype_color.scss b/dist/scss/overrides/_idtype_color.scss new file mode 100644 index 00000000..bec90f7e --- /dev/null +++ b/dist/scss/overrides/_idtype_color.scss @@ -0,0 +1,8 @@ + +// @import "~tdp_core/dist/scss/abstracts/mixins"; + +* { + @include idtype_color('Ensembl', rgb(127, 201, 127)); + @include idtype_color('Tissue', rgb(190, 174, 212)); + @include idtype_color('Cellline', rgb(253, 192, 134)); +} diff --git a/dist/scss/overrides/_select2.scss b/dist/scss/overrides/_select2.scss new file mode 100644 index 00000000..2d453a77 --- /dev/null +++ b/dist/scss/overrides/_select2.scss @@ -0,0 +1,16 @@ + +@at-root { + .select2-results__option, + .select2-selection__rendered { + .option-muted { + font-size: 13px; + color: #999; + } + + &.select2-results__option--highlighted { + .option-muted { + color: #afcde9; + } + } + } +} diff --git a/dist/views/SimilarityView.d.ts b/dist/views/SimilarityView.d.ts new file mode 100644 index 00000000..fd708ef3 --- /dev/null +++ b/dist/views/SimilarityView.d.ts @@ -0,0 +1,25 @@ +/** + * Created by Samuel Gratzl on 29.01.2016. + */ +import { IARankingViewOptions, ISelection, IViewContext, ARankingView, IAdditionalColumnDesc } from 'tdp_core'; +import { LocalDataProvider } from 'lineupjs'; +export declare class SimilarityView extends ARankingView { + private loader; + constructor(context: IViewContext, selection: ISelection, parent: HTMLElement, options?: Partial); + protected getParameterFormDescs(): import("tdp_core").IFormElementDesc[]; + get itemIDType(): import("visyn_core/idtype").IDType; + private updateOptionsData; + static convertData(data: string): { + [key: string]: any; + }[]; + private loadImpl; + private load; + protected getColumnDescs(columns: any[]): IAdditionalColumnDesc[]; + protected loadColumnDesc(): Promise; + protected loadRows(): Promise; + protected parameterChanged(name: string): Promise; + protected selectionChanged(): Promise; + private updateImpl; + protected createInitialRanking(provider: LocalDataProvider): void; +} +//# sourceMappingURL=SimilarityView.d.ts.map \ No newline at end of file diff --git a/dist/views/SimilarityView.d.ts.map b/dist/views/SimilarityView.d.ts.map new file mode 100644 index 00000000..dbe24125 --- /dev/null +++ b/dist/views/SimilarityView.d.ts.map @@ -0,0 +1 @@ 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+++ b/dist/views/UniProtProxyView.js @@ -7,7 +7,7 @@ import { GeneProxyView } from './GeneProxyView'; /** * helper view for proxying an existing external website */ -export class UniProtProxyView extends GeneProxyView { +class UniProtProxyView extends GeneProxyView { initImpl() { super.initImpl(); this.$node.classed('proxy_view', true); @@ -117,4 +117,5 @@ export class UniProtProxyView extends GeneProxyView { } UniProtProxyView.SELECTED_UNIPROT_ITEM = 'externalUniProt'; UniProtProxyView.OUTPUT_IDTYPE = 'UniProt_human'; +export { UniProtProxyView }; //# sourceMappingURL=UniProtProxyView.js.map \ No newline at end of file diff --git a/dist/views/UniProtProxyView.js.map b/dist/views/UniProtProxyView.js.map index 1ac07cd8..b70848b0 100644 --- a/dist/views/UniProtProxyView.js.map +++ b/dist/views/UniProtProxyView.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/views/ViewUtils.js b/dist/views/ViewUtils.js index 78f12138..d24ac93f 100644 --- a/dist/views/ViewUtils.js +++ b/dist/views/ViewUtils.js @@ -3,7 +3,7 @@ import { ColumnDescUtils } from 'tdp_core'; import { zipWith } from 'lodash'; import { scale as d3Scale } from 'd3v3'; import { FieldUtils } from '../providers'; -export class ViewUtils { +class ViewUtils { static integrateColors(scale, colors) { const old = new Set(scale.domain()); colors = Array.from(new Set(colors.filter((d) => Boolean(d) && !old.has(d)))); // just valid ones @@ -104,4 +104,5 @@ ViewUtils.base = d3Scale.category20().range().slice(); // splice out the orange ViewUtils.removed = ViewUtils.base.splice(2, 2); // reorder such that repeat after the primary colors ViewUtils.colors = ViewUtils.base.filter((d, i) => i % 2 === 0).concat(ViewUtils.base.filter((d, i) => i % 2 === 1)); +export { ViewUtils }; //# sourceMappingURL=ViewUtils.js.map \ No newline at end of file diff --git a/dist/views/ViewUtils.js.map b/dist/views/ViewUtils.js.map index 987a01d3..77b73a71 100644 --- a/dist/views/ViewUtils.js.map +++ b/dist/views/ViewUtils.js.map @@ -1 +1 @@ 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