Gene isobaric plots added

src/backend/mstulos/urls.py

@@ -15,5 +15,6 @@
         path('upload/done/', views.upload_done, name='upload_done'),
         path('plotdata/peptides/', views.fetch_plotdata_peptides),
         path('plotdata/psms/', views.fetch_plotdata_psms),
+        path('plotdata/genes/', views.fetch_plotdata_genes),
         ]
 

src/backend/mstulos/views.py

@@ -372,6 +372,36 @@ def frontpage(request):
     return render(request, 'mstulos/front_pep.html', context=context)
 
 
+@login_required
+@require_POST
+def fetch_plotdata_genes(request):
+    '''As fetch_plotdata_peptides, but with only isobaric values,
+    which is the only thing we store'''
+    data = json.loads(request.body.decode('utf-8'))
+    ## Only the isobaric quant values
+    ## First map the channel / sample / set names
+    channel_samples = {x: {} for x in data['expids']}
+    ctypes = m.Condition.Condtype
+    for cond in m.Condition.objects.filter(experiment_id__in=data['expids'], cond_type=ctypes.CHANNEL):
+        channel_samples[cond.pk] = {'name': cond.name, 'exp': cond.experiment_id}
+        for pc in cond.parent_conds.all():
+            ctype = ctypes(pc.cond_type).name
+            channel_samples[cond.pk][ctype] = pc.name
+
+    genemap = {x.pk: x.name for x in m.Gene.objects.filter(pk__in=data['gids'])}
+    # DB fetch isoquant peptides and put in list
+    iso = m.GeneIsoQuant.objects.filter(gene__pk__in=data['gids'],
+            channel__experiment__pk__in=data['expids']
+            ).annotate(ch=F('channel')).values('ch', 'gene', 'value')
+
+    return JsonResponse({'conditions': {x.value: x.label for x in ctypes},
+        'chmap': channel_samples,
+        'experiments': {x.pk: x.analysis.name for x in m.Experiment.objects.filter(pk__in=data['expids'])},
+        'genemap': genemap,
+        'isobaric': [x for x in iso],
+        })
+
+
 @login_required
 @require_POST
 def fetch_plotdata_peptides(request):

src/frontend/mstulos/src/App.svelte

@@ -3,6 +3,7 @@
 import { onMount } from 'svelte';
 import Tablerow from './Tablerow.svelte';
 import Plots from './Plots.svelte'
+import GenePlots from './GenePlots.svelte'
 import AggPlotsPep from './AggregatePlots.svelte'
 import AggPlotsPSM from './AggregatePlotsPSM.svelte'
 
@@ -302,12 +303,15 @@ onMount(async() => {
   <div>
   <p class="is-size-5">Plot {nr_filtered_pep} peptide{nr_filtered_pep > 1 ? 's' : ''} over {nr_filtered_exp} experiment{nr_filtered_exp > 1 ? 's' : ''}</p>
   <button class="button" on:click={e => switchPlot('peptides')}>Peptides</button>
+  <button class="button" on:click={e => switchPlot('genes')}>Gene</button>
   <button class="button" on:click={e => switchPlot('aggregates_pep')}>Aggregated peptides</button>
   <button class="button" on:click={e => switchPlot('aggregates_psm')}>Aggregated PSMs</button>
   </div>
 
   {#if showplots.peptides}
   <Plots />
+  {:else if showplots.genes}
+  <GenePlots />
   {:else if showplots.aggregates_pep}
   <AggPlotsPep />
   {:else if showplots.aggregates_psm}

src/frontend/mstulos/src/Plots.svelte

@@ -4,7 +4,7 @@ import { postJSON } from '../../datasets/src/funcJSON.js'
 import * as Plot from '@observablehq/plot';
 
 // data is already top lvl on the document so need no passing in here
-let plots
+let plots;
 let errors = [];
 
 async function fetchData() {