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moriondo2022moriondo2022
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Merge pull request #1014 from broadinstitute/sysbio-typo
Sysbio typo
2 parents 603050f + 9831a77 commit c9d57bd

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4 files changed

+80
-17
lines changed

4 files changed

+80
-17
lines changed

‎src/portals/SysBio/components/BulkTable.vue‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -36,9 +36,6 @@
3636
:fields="config.fields"
3737
:per-page="perPage"
3838
:current-page="currentPage"
39-
:sort-by="isSubtable? 'sample_id' : '-log10P'"
40-
:sort-desc="!isSubtable"
41-
:sort-icon-left="true"
4239
:tbody-tr-class="rowClasses"
4340
>
4441
<template #cell(gene)="r">
@@ -366,13 +363,15 @@ export default Vue.component("bulk-table", {
366363
return "";
367364
},
368365
async findGene(gene){
366+
console.log("Finding" + gene);
369367
// Populate the subtable before toggling it open
370368
let dataItem = this.bulkData.find(g => g.gene === gene);
371369
if (!dataItem){
372370
return;
373371
}
374372
//await this.getSubtable(dataItem);
375373
let location = this.allGenes.indexOf(gene);
374+
console.log(JSON.stringify(this.allGenes[0]));
376375
if (location === -1){
377376
return;
378377
}
@@ -392,6 +391,9 @@ export default Vue.component("bulk-table", {
392391
},
393392
downregulatedGenes(newGenes){
394393
this.$emit("downGenes", newGenes);
394+
},
395+
currentData(newData){
396+
console.log("Current data is:", JSON.stringify(newData));
395397
}
396398
}
397399
});

‎src/portals/SysBio/css/sysbio.css‎

Lines changed: 50 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -300,4 +300,53 @@ div.filtering-ui-content div.col.filter-col-sm input {
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background-color: #30b7f6;
301301
border: solid 1px #30b7f6;
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color: #fff !important;
303-
}
303+
}
304+
305+
/* Download image icon settings from mdkp.css*/
306+
.download-images-setting {
307+
position: absolute;
308+
top: -10px;
309+
right: 5px;
310+
}
311+
312+
.download-images-setting .options-gear {
313+
color: #333333;
314+
padding: 3px 10px;
315+
border-radius: 15px;
316+
font-size: 12px;
317+
margin-right: 10px;
318+
border: solid 1px #dddddd;
319+
}
320+
321+
.download-images-setting .options-gear>svg {
322+
font-size: 12px !important;
323+
}
324+
325+
.download-images-setting:hover .options-gear {
326+
color: #000000;
327+
}
328+
329+
.download-images-setting ul.options {
330+
display: none;
331+
position: absolute;
332+
background-color: #ffffff;
333+
padding: 15px;
334+
border: solid 1px #dddddd;
335+
border-radius: 5px;
336+
z-index: 10;
337+
list-style: none;
338+
right: 0;
339+
box-shadow: 0px 5px 5px 5px rgb(0 0 0 / 20%)
340+
}
341+
342+
.download-images-setting ul.options li {
343+
white-space: nowrap;
344+
}
345+
346+
.download-images-setting ul.options li label {
347+
padding-left: 5px;
348+
}
349+
350+
.download-images-setting:hover ul.options {
351+
display: block;
352+
}

‎src/portals/SysBio/views/BulkBrowser/Template.vue‎

Lines changed: 21 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,8 @@
2525
</div>
2626
<div class="tabs-section-wrapper">
2727
<div class="tab-section">
28-
<select v-model="$store.state.selectedCompType">
28+
<select v-model="$store.state.selectedCompType"
29+
class="form-control">
2930
<option value="">Select a comparison type</option>
3031
<option v-for="type in $parent.comptypes"
3132
:value="type">
@@ -43,7 +44,8 @@
4344
</div>
4445
<div class="tabs-section-wrapper">
4546
<div class="tab-section">
46-
<select v-model="$store.state.selectedAMP">
47+
<select v-model="$store.state.selectedAMP"
48+
class="form-control">
4749
<option value="">Select an AMP</option>
4850
<option v-for="amp in $parent.amps"
4951
:value="amp">
@@ -56,23 +58,24 @@
5658
<div class="tabs-group">
5759
<div class="tabs-wrapper">
5860
<div class="tab">
59-
Select a comparison
61+
Select a cell type
6062
</div>
6163
</div>
6264
<div class="tabs-section-wrapper">
6365
<div class="tab-section">
64-
<select v-model="$store.state.selectedComparison">
65-
<option value="">Select a comparison</option>
66+
<select v-model="$store.state.selectedComparison"
67+
class="form-control">
68+
<option value="">Select a cell type</option>
6669
<option v-for="comp in $parent.comparisons"
6770
:value="comp">
68-
{{ $store.state.currentComparisons[comp].label
71+
{{ $store.state.currentComparisons[comp].cellType
6972
}}
7073
</option>
7174
</select>
7275
</div>
7376
</div>
7477
</div>
75-
<!-- <div class="tabs-group">
78+
<div class="tabs-group">
7679
<div class="tabs-wrapper">
7780
<div class="tab">
7881
Search for a gene
@@ -93,12 +96,12 @@
9396
</div>
9497
<div class="tabs-section-wrapper">
9598
<div class="tab-section">
96-
<input type="number" step="0.1"
99+
<input type="number" step="0.1" class="form-control"
97100
:value=$parent.volcanoYCondition
98101
@change="event => $parent.setVolcano(event.target.value)"/>
99102
</div>
100103
</div>
101-
</div> -->
104+
</div>
102105
</div>
103106
</div>
104107
<div v-if="$parent.dataReady">
@@ -455,12 +458,19 @@ button.hide-table {
455458
}
456459
#menu {
457460
display: flex;
461+
border-radius: 5px;
462+
border: 1px solid darkgray;
463+
background-color: lightgray;
464+
padding: 10px;
458465
}
459466
#menu div.tabs-group {
460467
margin: 10px;
461-
max-width: 25%;
468+
border-radius: 5px;
462469
}
463470
#menu div.tabs-group:last-child {
464-
margin-right: 0px !important;
471+
min-width: 20%;
472+
}
473+
#gene-box {
474+
padding: 10px !important;
465475
}
466476
</style>

‎src/portals/SysBio/views/BulkBrowser/main.js‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -53,14 +53,15 @@ new Vue({
5353
allMetadata: null,
5454
bulkMetadata: null,
5555
plotId: "bulk_heatmap",
56-
plotHeight: 300,
56+
plotHeight: 450,
5757
chart: null,
5858
chartWidth: 0,
5959
datasets: [],
6060
truncateEnrichr: 10,
6161
enrichrUp: [],
6262
enrichrDown: [],
6363
enrichrLibraries: [],
64+
enrichrByor: "matkp_enrichrlibraries", // Using MATKP list until further notice
6465
enrichrLibrary: "KEGG_2015", //hardcoding default
6566
libraryPage: 1,
6667
selectedLibraryType: "",
@@ -182,7 +183,7 @@ new Vue({
182183
"x axis label": "log2 Fold Change",
183184
"y axis field": "-log10P",
184185
"y axis label": "-log10(FDR adj. p)",
185-
"width": 600,
186+
"width": 900,
186187
"height": this.plotHeight,
187188
"x condition": {
188189
"combination": "or",
@@ -287,6 +288,7 @@ new Vue({
287288
keyParams.set({ gene: this.$store.state.selectedGene });
288289
}
289290
this.getParams();
291+
this.enrichrLibraries = await getTextContent(this.enrichrByor);
290292
await this.$store.dispatch("queryBulkFile");
291293
await this.populateEnrichr();
292294
this.dataReady = true;

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