Merge pull request #51 from sonyahanson/master

[WIP] Doing some plotting of free energy results.

data/DMSO-backfill/making_figs.py

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+# This is a script version of DMSO-backfill.ipynb
+
+from assaytools import platereader
+import matplotlib.pyplot as plt
+import string
+import numpy as np
+
+part1 = "p38_singlet1_20160420_153238.xml"
+part2 = "p38_singlet2_20160420_154750.xml"
+
+part1_data = platereader.read_icontrol_xml(part1)
+part2_data = platereader.read_icontrol_xml(part2)
+
+part1_data_C = platereader.select_data(part1_data, '280_480_TOP_120', 'C')
+part1_data_D = platereader.select_data(part1_data, '280_480_TOP_120', 'D')
+part1_data_K = platereader.select_data(part1_data, '280_480_TOP_120', 'K')
+part1_data_L = platereader.select_data(part1_data, '280_480_TOP_120', 'L')
+
+well = dict()
+for j in string.ascii_uppercase:
+    for i in range(1,25):
+        well['%s' %j + '%s' %i] = i
+
+Lstated = np.array([20.0e-6,14.0e-6,9.82e-6,6.88e-6,4.82e-6,3.38e-6,2.37e-6,1.66e-6,1.16e-6,0.815e-6,0.571e-6,0.4e-6,0.28e-6,0.196e-6,0.138e-6,0.0964e-6,0.0676e-6,0.0474e-6,0.0320e-6,0.0240e-6,0.0160e-6,0.0120e-6,0.008e-6,0.00001e-6], np.float64) # ligand concentration, M
+
+# Stated concentrations of protein and ligand.
+Pstated = 0.5e-6 * np.ones([24],np.float64) # protein concentration, M
+
+# Assay configuration details
+import math
+assay_volume = 50e-6 # assay volume, L
+well_area = 0.1369 # well area, cm^2 for 4ti-0203 [http://4ti.co.uk/files/3113/4217/2464/4ti-0201.pdf]
+path_length = assay_volume * 1000 / well_area # cm, needed for inner filter effect corrections     
+
+# Uncertainties in protein and ligand concentrations.
+dPstated = 0.35 * Pstated # protein concentration uncertainty
+dLstated = 0.08 * Lstated # ligand concentraiton uncertainty (due to gravimetric preparation and HP D300 dispensing)
+
+def reorder2list(data,wells):
+
+    sorted_keys = sorted(well.keys(), key=lambda k:well[k])
+
+    reorder_data = []
+
+    for key in sorted_keys:
+        try:
+            reorder_data.append(data[key])
+        except:
+            pass
+
+    reorder_data = np.asarray(reorder_data,np.float64)
+
+    return reorder_data
+
+def quick_model(protein_data, buffer_data,name):
+    reorder_protein = reorder2list(protein_data,well)
+    reorder_buffer = reorder2list(buffer_data,well)
+
+    print name   
+
+    from assaytools import pymcmodels
+    pymc_model = pymcmodels.make_model(Pstated, dPstated, Lstated, dLstated, 
+               top_complex_fluorescence=reorder_protein,
+               top_ligand_fluorescence=reorder_buffer,
+               use_primary_inner_filter_correction=True, 
+               use_secondary_inner_filter_correction=True, 
+               assay_volume=assay_volume, DG_prior='uniform')
+
+    mcmc = pymcmodels.run_mcmc(pymc_model)
+
+    from assaytools import plots
+    figure = plots.plot_measurements(Lstated, Pstated, pymc_model, mcmc=mcmc)
+
+    map = pymcmodels.map_fit(pymc_model)
+
+    pymcmodels.show_summary(pymc_model, map, mcmc)
+
+    DeltaG = map.DeltaG.value
+
+    np.save('DeltaG_%s.npy'%name,DeltaG)
+    np.save('DeltaG_trace_%s.npy'%name,mcmc.DeltaG.trace())
+
+
+quick_model(part1_data_C,part1_data_D,'BSI_w_backfill')
+
+quick_model(part1_data_K,part1_data_L,'BSI')
+
+DeltaG_trace_BSI_w_backfill = np.load('DeltaG_trace_BSI_w_backfill.npy')
+DeltaG_trace_BSI = np.load('DeltaG_trace_BSI.npy')
+
+plt.clf()
+
+plt.hist(DeltaG_trace_BSI, 40, alpha=0.75, label='Bsi no backfill')
+plt.hist(DeltaG_trace_BSI_w_backfill, 40, alpha=0.75, label='Bsi with backfill')
+plt.plot([DeltaG_trace_BSI_w_backfill.mean(),DeltaG_trace_BSI_w_backfill.mean()],[0, 350],'g-')
+plt.plot([DeltaG_trace_BSI.mean(),DeltaG_trace_BSI.mean()],[0, 350],'b-')
+#plt.plot([literature_Bos,literature_Bos],[0, 350],'r-',label='IUPHARM data')
+plt.xlabel('$\Delta G$ ($k_B T$)');
+plt.ylabel('$P(\Delta G)$');
+plt.title('histogram of estimates for binding free energy');
+plt.legend(loc=0);
+
+plt.savefig('BSI_w_backfill.png')

data/spectra/README.md

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+# Spectra Data
+
+Right now this is a duplicate of some of the data in `assaytools/examples/ipynbs/data-analysis/spectra/`.
+
+
+
+
+