Test bin peaks

mdb/spectra/migrations/0008_auto_20210611_0041.py

@@ -0,0 +1,21 @@
+# Generated by Django 3.1 on 2021-06-11 00:41
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('spectra', '0007_auto_20210609_2238'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='binnedpeaks',
+            name='peak_intensity',
+        ),
+        migrations.RemoveField(
+            model_name='collapsedcosinescore',
+            name='binned_peaks',
+        ),
+    ]

mdb/spectra/models.py

@@ -239,11 +239,9 @@ class BinnedPeaks(models.Model):
   Binned peaks version of a spectra when matched against set of spectra.
   '''
   peak_mass = models.TextField(blank = True)
-  peak_intensity = models.TextField(blank = True)
   peak_snr = models.TextField(blank = True)
   spectra = models.ForeignKey(
     'CollapsedSpectra',
-    # ~ related_name = 'spectra',
     on_delete = models.CASCADE)
 
 # ~ class CollapsedCosineScore(AbstractCosineScore):
@@ -253,14 +251,14 @@ class CollapsedCosineScore(models.Model):
   '''
   spectra = models.ForeignKey(
     'CollapsedSpectra',
-    # ~ related_name = 'spectra',
     on_delete = models.CASCADE)
   library = models.ForeignKey(
     'chat.Library',
     on_delete = models.CASCADE)
   scores = models.TextField()
   spectra_ids = models.TextField()
-  binned_peaks = models.ManyToManyField('BinnedPeaks')
+  #intensities = models.TextField()
+  #binned_peaks = models.ManyToManyField('BinnedPeaks')
 
 # ~ class CollapsedCosineScore(AbstractCosineScore):
   # ~ spectra1 = models.ForeignKey(

mdb/spectra_search/views.py

@@ -158,8 +158,7 @@ def process_file(request, file, form, owner):
   n2 = CollapsedSpectra.objects.filter(
     library__exact = form.cleaned_data['search_library'].id,
     spectra_content__exact = 'PR'
-    #max_mass__gt = 6000
-  ).values('id')
+  ).order_by('id').values('id')#, 'strain_id')
   data = {
     'ids': [n1.id] + [s['id'] for s in list(n2)]
   }
@@ -168,7 +167,27 @@ def process_file(request, file, form, owner):
     params = data
   )
 
-  print('bp', r.json()['binnedPeaks'][1][0])
+  print('bp', r.json()['binnedPeaks'])
+  # ~ print('bp', r.json()['binnedPeaks']['intensity.233'])
+  # ~ print('bp', r.json()['binnedPeaks']['intensity.233'][0])
+  # ~ print('bp', r.json()['colnames'])
+  tmp = r.json()['binnedPeaks']
+  binned_peaks = {}
+  # ~ count = 0
+  for v in tmp: # Dictionary of binned peaks
+    binned_peaks[str(v['csId'][0])] = {
+      'mass': v['mass'],
+      'intensity': v['intensity'],
+      'snr': v['snr'],
+    }
+    # ~ else:
+      # ~ c = str(count)
+      # ~ binned_peaks[v['csId.' + c][0]] = {
+        # ~ 'mass': v['mass.' + c],
+        # ~ 'intensity': v['intensity.' + c],
+        # ~ 'snr': v['snr.' + c],
+      # ~ }
+    # ~ count += 1
 
 # ~ # test
 # ~ from spectra.models import *
@@ -188,7 +207,7 @@ def process_file(request, file, form, owner):
   # ~ key = lambda x: (x[1], x[0]), reverse = True)
 # ~ )
 
-  # create a dictionary and sort by its values
+  # Dictionary sorted by its values
   from collections import OrderedDict
   k = [str(s['id']) for s in list(n2)] # one less
   v = r.json()['similarity'][1:] # one more remove first???
@@ -209,6 +228,9 @@ def process_file(request, file, form, owner):
       'original': {
         'peak_mass': n1.peak_mass,
         'peak_intensity': n1.peak_intensity,
+        'binned_mass': binned_peaks[str(n1.id)]['mass'],
+        'binned_intensity': binned_peaks[str(n1.id)]['intensity'],
+        'binned_snr': binned_peaks[str(n1.id)]['snr'],
       }
     }
 
@@ -233,6 +255,9 @@ def process_file(request, file, form, owner):
         'rowcount': rowcount,
         'peak_mass': cs.peak_mass,
         'peak_intensity': cs.peak_intensity,
+        'binned_mass': binned_peaks[str(cs.id)]['mass'],
+        'binned_intensity': binned_peaks[str(cs.id)]['intensity'],
+        'binned_snr': binned_peaks[str(cs.id)]['snr'],
       })
       rowcount += 1
     ws.send(json.dumps(l))

rplumber/plumber.R

@@ -81,18 +81,38 @@ function(req, ids) {
 
   binnedPeaks <- MALDIquant::binPeaks(allPeaks, tolerance = 0.002)
   featureMatrix <- MALDIquant::intensityMatrix(binnedPeaks, allSpectra)
-  # manual inspection...
-  print(toString(head(binnedPeaks, 2)))
+
+  b <- list()
+#~   allSpectra = list()
+#~   allPeaks = list()
+  for(i in 1:length(binnedPeaks)) {
+    s <- binnedPeaks[[i]]
+    b <- append(b, list(list(
+      'mass' = MALDIquant::mass(s),
+      'intensity' = MALDIquant::intensity(s),
+      'snr' = MALDIquant::snr(s),
+      'csId' = ids[[i]]
+    )))
+  }
+#~   print(mass(binnedPeaks[[1]]))
 #~   print(toString(binnedPeaks))
+#~   print(colnames(featureMatrix))
+#~   print(capture.output(featureMatrix))
   #print(toString(featureMatrix[1,]))
   #print(toString(featureMatrix[2,]))
   #print(coop::cosine(featureMatrix[1,], featureMatrix[2,]))
   d <- coop::cosine(t(featureMatrix))
   d <- round(d, 3)
 
-  return(list('similarity' = d[1,], 'binnedPeaks' = capture.output(binnedPeaks)))
+  return(list(
+    'similarity' = d[1,],
+    'binnedPeaks' = b
+#~     'binnedPeaks' = capture.output(toString(binnedPeaks))
+#~     'featureMatrix' = featureMatrix,
+#~     'colnames' = colnames(featureMatrix)
+  ))
 
-  return(d[1,])
+  #return(d[1,])
 
   emptyProtein <- unlist(
     lapply(allPeaks, MALDIquant::isEmpty)
@@ -269,8 +289,14 @@ dbSpectra <- function(ids) {
   allSpectra = list()
   allPeaks = list()
 
+  # q&d initial solution: require monotonically increasing ids
+  id <- 0
+
   for(i in 1:nrow(q)) {
     row <- q[i,]
+    if (row$id < id) {
+      stop('results not monotonic')
+    }
     allPeaks <- append(allPeaks,
       MALDIquant::createMassPeaks(
         mass = as.numeric(strsplit(row$peak_mass, ",")[[1]]),