chromaquant 0.3.1__py3-none-any.whl → 0.5.0__py3-none-any.whl

chromaquant/Manual/HydroUI.py

@@ -1,418 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-
-COPYRIGHT STATEMENT:
-
-ChromaQuant – A quantification software for complex gas chromatographic data
-
-Copyright (c) 2024, by Julia Hancock
-              Affiliation: Dr. Julie Elaine Rorrer
-	      URL: https://www.rorrerlab.com/
-
-License: BSD 3-Clause License
-
----
-
-SCRIPT WHICH RUNS A DESKTOP APPLICATION FOR FUTURE USE IN SPECTRA VISUALIZATION
-
-Julia Hancock
-Started 11/21/2023
-
-"""
-
-""" PACKAGES """
-import sys
-import pandas as pd
-#Dash and plotly – dcc = "Dash Core Components", px = "Plotly express" with visualization tools
-from dash import Dash, html, dash_table, dcc, callback, Output, Input
-from plotly.subplots import make_subplots
-import plotly.express as px
-import plotly.graph_objects as go
-from pubchempy import Compound, get_compounds
-from rdkit import Chem
-from rdkit.Chem.Draw import MolsToGridImage, MolDrawing, rdMolDraw2D
-import base64
-from io import BytesIO
-import os
-from molmass import Formula
-
-""" PARAMETERS """
-#Write sample name
-sname = "MBPR048_01"
-
-#Write whether sample is liquid ("L") or gas ("G")
-stype = "G"
-
-#Write whether there exists a file containing matched FID and MS peaks (True/False)
-smatchtf = False
-
-""" DIRECTORIES """
-#Current script directory
-script_directory = os.path.dirname(__file__)
-
-""" DATA IMPORTS """
-#Define file names using user parameters
-if stype == "G":
-    fn_FID_SPEC = sname+"_GS2_FID_SPEC.csv"
-    fn_MS_SPEC = sname+"_GS1_MS_SPEC.csv"
-    
-    if smatchtf == True:
-        fn_FPM = sname+"_GS2_FIDpMS.csv"
-    else:
-        fn_FPM = "default_FIDpMS.csv"
-
-if stype == "L":
-    fn_FID_SPEC = sname+"_LQ1_FID_SPEC.csv"
-    fn_MS_SPEC = sname+"_LQ1_MS_SPEC.csv"
-    
-    if smatchtf == True:
-        fn_FPM = sname+"_LQ1_FIDpMS.csv"
-    else:
-        fn_FPM = "default_FIDpMS.csv"
-
-#Define directories for desired dataframes
-DIR_LQ_FIDpMS_PeaksLB = "/Users/connards/Desktop/University/Rorrer Lab/Scripts/Quantification/data/"+sname+"/"+fn_FPM
-DIR_LQ_FID_SPEC = "/Users/connards/Desktop/University/Rorrer Lab/Scripts/Quantification/data/"+sname+"/"+fn_FID_SPEC
-DIR_LQ_MS_SPEC = "/Users/connards/Desktop/University/Rorrer Lab/Scripts/Quantification/data/"+sname+"/"+fn_MS_SPEC
-#Column names to add to imported spectral data
-col_names_SPEC = ['RT','Signal']
-
-#Read matched peak data between FID and MS
-LQ_FIDpMS_PeaksLB = pd.read_csv(DIR_LQ_FIDpMS_PeaksLB)
-
-#Read spectra data for FID
-LQ_FID_SPEC = pd.read_csv(DIR_LQ_FID_SPEC, names=col_names_SPEC, header=None)
-#Add column labeling FID data
-LQ_FID_SPEC['SignalType'] = 'FID'
-
-#Read spectra data for MS
-LQ_MS_SPEC = pd.read_csv(DIR_LQ_MS_SPEC, names=col_names_SPEC, header=None)
-#Add column labeling MS data
-LQ_MS_SPEC['SignalType'] = 'MS'
-
-#Get dictionary of checklist entries to SignalType entries
-dictSPEC = {'FID':'FID','MS':'MS'}
-#Get list of checklist keys
-dictSPEC_keys = list(dictSPEC.keys())
-
-#Append MS dataframe to FID dataframe
-LQ_FIDpMS_SPEC = pd.concat([LQ_FID_SPEC,LQ_MS_SPEC],ignore_index=True)
-
-""" ACCESSING PUBCHEM """
-
-#If there exists FIDpMS files, proceed
-if smatchtf == True:
-    #Create a copy of the PeaksLB dataframe called PeaksLB_SMILES
-    PeaksLB_Smiles = LQ_FIDpMS_PeaksLB.copy()
-    #Read the existing smilePairs.csv
-    smilePairs = pd.read_csv(os.path.join(script_directory,'resources','smilePairs.csv'))
-    #Add a column to the PeaksLB dataframe with the smiles of matched compounds, ignoring 'No match'
-    PeaksLB_Smiles['isoSMILES'] = ''
-    #List of indices with compound names
-    compindex = []
-    #Set up temporary smile string for use in for loop
-    tempSmile = smilePairs.loc[smilePairs['Compound Name']==PeaksLB_Smiles.at[4,'Compound Name']]
-
-    #Loop through all rows in PeaksLB_Smiles
-    print('[MAIN] Assessing compound structures through SMILES...')
-    for i, row in PeaksLB_Smiles.iterrows():
-        
-        #Only add peaks with matched compounds
-        if PeaksLB_Smiles.at[i,'Compound Name'] != 'No match' and PeaksLB_Smiles.at[i,'Compound Name'] != 'No Match':
-            
-            #Try/except to catch error in accessing dataframe
-            try:
-                #If the compound name can be found in the compound-SMILES .csv file, add to dataframe
-                if any(smilePairs['Compound Name']==row['Compound Name']):
-                    tempSmile = smilePairs.loc[smilePairs['Compound Name']==row['Compound Name'],'isoSMILES']
-                    #Choose the first SMILES in the series
-                    tempSmile = tempSmile[tempSmile.index[0]]
-                    #Save SMILES to PeaksLB_Smiles dataframe
-                    PeaksLB_Smiles.at[i,'isoSMILES'] = tempSmile
-                #If the compound isn't in the list, get SMILES from PubCHEM
-                else:
-                    PeaksLB_Smiles.at[i,'isoSMILES'] = get_compounds(PeaksLB_Smiles.at[i,'Compound Name'],\
-                                                                     'name')[0].isomeric_smiles
-                    print('[MAIN] Downloading SMILES for {0}...'.format(PeaksLB_Smiles.at[i,'Compound Name']))
-                    compindex.append(i)
-                    
-            except:
-                print('[ERROR] An error occurred in accessing SMILES for {0}'.format(row['Compound Name']))
-
-        else:
-            pass
-
-    #If any compounds were previously unlabelled, save the compound name and SMILES pairs as a .csv
-    smilePairsOut = pd.concat([smilePairs,PeaksLB_Smiles.loc[compindex,['Compound Name','isoSMILES']]],ignore_index=True)
-    if smilePairsOut.size > smilePairs.size:
-        print("[MAIN] Saving updated compound-SMILES pairs...")
-        smilePairsOut.to_csv(os.path.join(script_directory,'resources','smilePairs.csv'),index=False)
-    else:
-        pass
-
-
-    """ LABELLING SPECTRA """
-    print("[MAIN] Labelling the FID spectrum using the peak-compound dataframe...")
-    #Find only the PeaksLB_Smiles rows which have compound matches
-    PeaksLB_Smiles = PeaksLB_Smiles[~PeaksLB_Smiles['Compound Name'].isin(['No Match','No match'])]
-    #For every entry in this new PeaksLB_Smiles dataframe, find the nearest FID Spectra RT to the labelled peak RT's
-    for i, row in PeaksLB_Smiles.iterrows():
-        #Find the closest row index in LQ_FID_SPEC
-        df_closestIN = LQ_FID_SPEC.iloc[(LQ_FID_SPEC['RT']-row['FID RT']).abs().argsort()[:1]].index[0]
-        #Add four columns to the spectral data: compound name, formula, match factor, and isosmiles
-        LQ_FID_SPEC.at[df_closestIN,'Compound Name'] = row['Compound Name']
-        LQ_FID_SPEC.at[df_closestIN,'Formula'] = row['Formula']
-        LQ_FID_SPEC.at[df_closestIN,'Match Factor'] = row['Match Factor']
-        LQ_FID_SPEC.at[df_closestIN,'isoSMILES'] = row['isoSMILES']
-        #Find the molecular weight of the given compound and assign to a new column in the spectral data
-        LQ_FID_SPEC.at[df_closestIN,'MW'] = Formula(row['Formula']).mass
-
-#Otherwise, pass
-else:
-    pass
-
-""" WEB APPLICATION """
-
-#Initialize the application with the Dash constructor
-app = Dash(__name__)
-
-#App layout
-app.layout = html.Div([
-    
-    #First row
-    html.Div(children=[
-        #First row first column
-        html.Div(children=[
-        #Scatter plot inside of a dcc interactive figure module
-        dcc.Graph(id='controls_and_graph')],\
-                  style={'display':'inline-block','vertical-align':'top','margin-left': 5,'margin-top': '3vw','width':'70%'}),
-        
-        #First row second column
-        html.Div(children=[
-            #Checklist for selecting viewed data
-            html.Div(children=[dcc.Checklist(dictSPEC_keys,[dictSPEC_keys[0]],id='controls_and_checklist')],style={'margin-top':100},className='row'),
-            #Axis limit entries
-            #x limit lower
-            html.Div(children=[dcc.Input(id='xlim_l',type='number',placeholder='Lower x-limit')],style={'margin-top':20},className='row'),
-            #x limit upper
-            html.Div(children=[dcc.Input(id='xlim_u',type='number',placeholder='Upper x-limit')],className='row'),
-            #y limit lower
-            html.Div(children=[dcc.Input(id='ylim_l',type='number',placeholder='Lower y-limit')],className='row'),
-            #y limit upper
-            html.Div(children=[dcc.Input(id='ylim_u',type='number',placeholder='Upper y-limit')],className='row'),
-            #y2 limit lower
-            html.Div(children=[dcc.Input(id='y2lim_l',type='number',placeholder='Secondary Lower y-limit')],className='row'),
-            #y2 limit upper
-            html.Div(children=[dcc.Input(id='y2lim_u',type='number',placeholder='Secondary Upper y-limit')],className='row')],
-        
-        #Set display style to inline-block
-        style={'display':'inline-block','vertical-align':'middle','margin-left': 0,'margin-top': '3vw','width':'25%'})],
-        className='row'),
-    
-    #Second row
-    html.Div(children=[
-        #Compound structure image
-        html.Img(id='structure-image')],className='row')
-    
-    ])
-
-""" CALLBACK CONTROLS """
-#FID and MS spectra selection and axis limits callback
-@callback(
-    Output(component_id='controls_and_graph',component_property='figure'),
-    Input(component_id='controls_and_checklist',component_property='value'),
-    Input('xlim_l','value'),
-    Input('xlim_u','value'),
-    Input('ylim_l','value'),
-    Input('ylim_u','value'),
-    Input('y2lim_l','value'),
-    Input('y2lim_u','value')
-)
-#Callback graph updating function
-def update_graph(fig_chosen,xlim_lval,xlim_uval,ylim_lval,ylim_uval,y2lim_lval,y2lim_uval):
-    #Format axis limits into a list
-    axLim = [xlim_lval,xlim_uval,ylim_lval,ylim_uval,y2lim_lval,y2lim_uval]
-    #Dictionary of colors for specific use for MS and FID spectra
-    colorDict = {'FID':px.colors.qualitative.Safe[4],'MS':px.colors.qualitative.Safe[1]}
-    #List of applicable dataframe titles based on fig_chosen as keys in dictSPEC
-    fig_chosen_dictSPEC = [dictSPEC[i] for i in fig_chosen]
-    #Filter DataFrame based on fig_chosen
-    #filDF = LQ_FIDpMS_SPEC[LQ_FIDpMS_SPEC['SignalType'].isin(fig_chosen_dictSPEC)]
-    
-    #Initialize figure
-    fig = make_subplots(specs=[[{'secondary_y': True}]])
-    #If there are any spectra chosen, plot them
-    if len(fig_chosen) != 0:
-        #Add a trace to the figure for each entry in fig_chosen
-        for i in range(len(fig_chosen_dictSPEC)):
-            #If the entry is past the first, set secondary_y axis value to True, otherwise set to False
-            if i > 0:
-                yTF = True
-            else:
-                yTF = False
-            #Filter DataFrame based on ith entry in fig_chosen_dictSPEC
-            filDF = LQ_FIDpMS_SPEC[LQ_FIDpMS_SPEC['SignalType'].str.match(fig_chosen_dictSPEC[i])]
-            
-            #Add a trace
-            fig.add_trace(go.Scattergl(x=filDF['RT'],y=filDF['Signal'],\
-                                     name=fig_chosen_dictSPEC[i],marker=dict(color=colorDict[fig_chosen[i]]),mode='lines+markers'),\
-                                     secondary_y=yTF)
-        
-        #Update figure layout by adding titles
-        fig.update_layout(title={'text':sname+' Spectra','font':{'color':'rgb(76, 46, 132)','size':20,'family':'Arial'}},\
-                                  legend_title='Displayed Spectra')
-        fig.update_xaxes(title_text='Retention time (min)')
-        fig.update_yaxes(title_text=fig_chosen_dictSPEC[0]+' Signal (a.u.)',secondary_y=False)
-        #Add a secondary y-axis title if necessary
-        if len(fig_chosen_dictSPEC) > 1:
-            fig.update_yaxes(title_text=fig_chosen_dictSPEC[1]+' Signal (a.u.)',secondary_y=True)
-            #Check if user-inputted axis limits are viable
-            #If lower ylim is less than upper ylim, update y-axis
-            #If any NoneType exist in the axis limits list, do not update limits
-            if None not in axLim[4:] and axLim[4] < axLim[5]:
-                fig.update_yaxes(range=[axLim[4],axLim[5]],secondary_y=True)
-            else:
-                pass
-        else:
-            pass
-    
-        #Check if user-inputted axis limits are viable
-        #If lower xlim is less than upper xlim, update x-axis
-        #If any NoneType exist in the axis limits list, do not update limits
-        if None not in axLim[:1] and axLim[0] < axLim[1]:
-            fig.update_xaxes(range=[axLim[0],axLim[1]])
-        else:
-            pass
-        #If lower ylim is less than upper ylim, update y-axis
-        #If any NoneType exist in the axis limits list, do not update limits
-        if None not in axLim[2:4] and axLim[2] < axLim[3]:
-            fig.update_yaxes(range=[axLim[2],axLim[3]],secondary_y=False)
-        else:
-            pass
-        
-    #If no spectra are chosen, don't plot anything
-    else:
-        pass
-    
-    return fig
-
-
-#Compound structure drawing function
-@callback(
-    Output('structure-image','src'),
-    Input('controls_and_graph','selectedData')
-)
-def draw_structure(selectedData):
-    max_structs = 6
-    empty_plot = "data:image/gif;base64,R0lGODlhAQABAAAAACwAAAAAAQABAAA="
-    
-    if selectedData:
-        #Take first point in selectedData, creating nested list
-        checkPoint = [selectedData['points'][0]['curveNumber'],\
-                       selectedData['points'][0]['x'],\
-                       selectedData['points'][0]['y']]
-
-        #Dictionary assigning each spectra to a curve number
-        specKeys = {'FID':'','MS':''}
-        
-        #Assign spectra to curve numbers according to whether or not the first point matches any points in the FID signal
-        try:
-            if checkPoint[2] == LQ_FID_SPEC.at[LQ_FID_SPEC[LQ_FID_SPEC['RT']==checkPoint[1]].index[0],'Signal']:
-                specKeys['FID'] = int(checkPoint[0])
-                specKeys['MS'] = int(not checkPoint[0])
-            else:
-                pass
-        except:
-            specKeys['FID'] = int(not checkPoint[0])
-            specKeys['MS'] = int(checkPoint[0])
-        
-        #Create list of selected points filtered so only FID results show
-        selectedFIDData = []
-        for i in selectedData['points']:
-            if i['curveNumber'] == specKeys['FID']:
-                selectedFIDData.append({'x':i['x'],'y':i['y'],'pointIndex':i['pointIndex']})
-        
-        if len(selectedFIDData) == 0:
-            return empty_plot
-        #List of selected point indices on FID spectrum
-        match_idx = [x['pointIndex'] for x in selectedFIDData]
-        #Dataframe with smiles and related data for selected points
-        smilesDF = LQ_FID_SPEC.loc[match_idx,['RT','Compound Name','Formula','Match Factor','isoSMILES']]
-        #Set FID spectra index to its own column and reset the indices
-        smilesDF.reset_index(inplace=True)
-        smilesDF = smilesDF.rename(columns={'index':'Spectra Index'})
-        #Filter dataframe to only include non-NaN smiles entries
-        smilesDF_F = smilesDF[smilesDF['isoSMILES'].notnull()].reset_index(drop=True)
-        #Get lists of smiles rdkit objects and corresponding compound names
-        list_smiles = [Chem.MolFromSmiles(x) for x in smilesDF_F['isoSMILES'].tolist()][:max_structs]
-        #Create a list of legend entries using data from smilesDF_F
-        list_legends = [smilesDF_F.loc[smilesDF_F.index[i],'Compound Name']+'\n'+\
-                        smilesDF_F.loc[smilesDF_F.index[i],'Formula']+' - '+\
-                        '{:.4}% Match'.format(smilesDF_F.loc[smilesDF_F.index[i],'Match Factor'])+'\n'+\
-                        '{:.3} min'.format(smilesDF_F.loc[smilesDF_F.index[i],'RT']) for i in range(len(smilesDF_F))][:max_structs]
-        #Initialize MolDraw2DCairo drawer
-        drawer = rdMolDraw2D.MolDraw2DCairo(1200,180,200,180)
-        #Set drawing options
-        drawer.drawOptions().useBWAtomPalette()
-        drawer.drawOptions().legendFontSize = 16
-        drawer.drawOptions().legendFraction = 0.3
-        drawer.drawOptions().maxFontSize = 16
-        drawer.drawOptions().padding = 0.05
-        drawer.drawOptions().centreMoleculesBeforeDrawing = True
-        #Draw the molecules
-        drawer.DrawMolecules(list_smiles,legends=list_legends)
-        drawer.FinishDrawing()
-        #Set buffered image using BytesIO encoding
-        buffered = BytesIO(drawer.GetDrawingText())
-        
-        #OLD METHOD FOR DRAWING GRID OF MOLECULE IMAGES
-        #Create a grid of molecule images using rdkit
-        #img = MolsToGridImage(list_smiles[0:max_structs], molsPerRow=structs_per_row, legends=list_legends, subImgSize=(300,300))
-        #img = SVG(drawer.GetDrawingText())
-        #Encode and save the image
-        #buffered = BytesIO()
-        #img.save(buffered, format="JPEG")
-        
-        #Encode the image
-        encoded_image = base64.b64encode(buffered.getvalue())
-        #Define and return the image string
-        src_str = 'data:image/png;base64,{}'.format(encoded_image.decode())
-        return src_str
-    else:
-        #Return a blank string
-        return ''
-
-""" EXECUTE APPLICATION """
-
-#Run the application
-if __name__ == '__main__':
-    app.run(debug=True)
-
-    
-"""
-#Callback controls
-@callback(
-    Output(component_id='controls_and_graph',component_property='figure'),
-    Input(component_id='controls_and_checklist',component_property='value')   
-)
-
-def update_graph(fig_chosen):
-    #List of applicable dataframe titles based on fig_chosen as keys in dictSPEC
-    fig_chosen_dictSPEC = [dictSPEC[i] for i in fig_chosen]
-    #Filter DataFrame based on fig_chosen
-    filDF = LQ_FIDpMS_SPEC[LQ_FIDpMS_SPEC['SignalType'].isin(fig_chosen_dictSPEC)]
-    fig = px.scatter(filDF,x='RT',y='Signal',color='SignalType',\
-                     color_discrete_sequence=[px.colors.qualitative.Safe[4],\
-                                              px.colors.qualitative.Safe[1]])
-    #Update figure layout
-    fig.update_layout(title='MBPR031 Spectra',xaxis_title='Retention time (min)',yaxis_title='Signal (a.u.)',legend_title='Displayed Spectra')
-    return fig
-"""
-    
-    
-    
-    
-    
-    
-