Add TicChromaogram

content/FLASHDeconv/FLASHDeconvLayoutManager.py

@@ -16,7 +16,8 @@
     'Raw spectrum (Scan table needed)',
     'Mass table (Scan table needed)',
     '3D S/N plot (Mass table needed)',
-    'Score Distribution Plot'
+    'Score Distribution Plot',
+    'TIC Chromatogram',
     # "Sequence view" and "Internal fragment map" is added when "input_sequence" is submitted
 ]
 
@@ -31,6 +32,7 @@
     'mass_table',
     '3D_SN_plot',
     'fdr_plot',
+    'tic_chromatogram',
     # "sequence view" and "internal fragment map" added when "input_sequence" is submitted
 ]
 

src/parse/deconv.py

@@ -45,7 +45,7 @@ def parseDeconv(
             )
 
             # Collect here as this is the data we are operating on
-            relevant_heatmap_lazy = relevant_heatmap_lazy.collect().lazy()
+            relevant_heatmap_lazy = relevant_heatmap_lazy.collect(streaming=True).lazy()
 
             # Get count for compression level calculation
             heatmap_count = relevant_heatmap_lazy.select(pl.len()).collect().item()
@@ -69,6 +69,32 @@ def parseDeconv(
                     dataset_id, f'ms{ms_level}_{descriptor}_heatmap_{size}',
                     current_heatmap_lazy
                 )
+
+    # Create TIC table
+    ms1_heatmap = file_manager.get_results(
+            dataset_id,  ['ms1_raw_heatmap'], use_polars=True
+    )['ms1_raw_heatmap']
+    ms1_heatmap = ms1_heatmap.with_columns(pl.lit(1).alias('level'))
+    ms1_heatmap = ms1_heatmap.drop(['mass', 'mass_idx'])
+    ms2_heatmap = file_manager.get_results(
+            dataset_id,  ['ms2_raw_heatmap'], use_polars=True
+    )['ms2_raw_heatmap']
+    ms2_heatmap = ms2_heatmap.with_columns(pl.lit(2).alias('level'))
+    ms2_heatmap = ms2_heatmap.drop(['mass', 'mass_idx'])
+    tic_data = pl.concat([ms1_heatmap, ms2_heatmap], how='vertical')
+    tic_data = (
+        tic_data.group_by('scan_idx')
+            .agg([
+                pl.col('rt').first().alias('rt'),
+                pl.col('level').first().alias('level'),
+                pl.col('intensity').sum().alias('tic'),
+            ])
+    )
+    tic_data = tic_data.sort("scan_idx", descending=False)
+    file_manager.store_data(dataset_id, 'tic', tic_data)
+
+
+
 
     logger.log("20.0 %", level=2)
 

src/render/components.py

@@ -99,3 +99,9 @@ class FLASHQuant:
     def __init__(self):
         self.title = 'QuantVis'
         self.componentName = 'FLASHQuantView'
+
+
+class Chromatogram:
+    def __init__(self):
+        self.title = 'TIC'
+        self.componentName = 'TICChromatogram'

src/render/compression.py

@@ -50,7 +50,7 @@ def downsample_heatmap(data, max_datapoints=20000, rt_bins=400, mz_bins=50, logg
     )
 
     # We need to collect here because scipy requires numpy arrays
-    sorted_data = sorted_data.collect()
+    sorted_data = sorted_data.collect(streaming=True)
 
     # Count peaks
     total_count = sorted_data.select(pl.count()).item()

src/render/initialize.py

@@ -3,7 +3,7 @@
 from src.render.components import (
     PlotlyHeatmap, PlotlyLineplot, PlotlyLineplotTagger, Plotly3Dplot, 
     Tabulator, SequenceView, InternalFragmentMap, FlashViewerComponent, 
-    FDRPlotly, FLASHQuant
+    FDRPlotly, FLASHQuant, Chromatogram
 )
 from src.render.compression import compute_compression_levels
 
@@ -172,6 +172,10 @@ def initialize_data(comp_name, selected_data, file_manager, tool):
         data = file_manager.get_results(selected_data,  ['quant_dfs'])
         data_to_send['quant_data'] = data['quant_dfs']
         component_arguments = FLASHQuant()
+    elif comp_name == 'tic_chromatogram':
+        data = file_manager.get_results(selected_data,  ['tic'])
+        data_to_send['tic'] = data['tic']
+        component_arguments = Chromatogram()
 
     components = [[FlashViewerComponent(component_arguments)]]