.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples\liver\plot_tristan_patients.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_liver_plot_tristan_patients.py: ===================================================================== Clinical - rifampicin effect in subjects with impaired liver function ===================================================================== The data show in this example aimed to demonstrates the effect of rifampicin on liver function of patients with impaired function. The use case is provided by the liver work package of the `TRISTAN project `_ which develops imaging biomarkers for drug safety assessment. The data were acquired in the aorta and liver in 3 patients with dynamic gadoxetate-enhanced MRI. The study participants take rifampicin as part of their routine clinical workup, with an aim to promote their liver function. For this study, they were taken off rifampicin 3 days before the first scan, and placed back on rifampicin 3 days before the second scan. The aim was to determine the effect if rifampicin in uptake and excretion function of the liver. The data confirmed that patients had significantly reduced uptake and excretion function in the absence of rifampicin. Rifampicin adminstration promoted their excretory function but had no effect on their uptake function. Reference --------- Manuscript in preparation.. .. GENERATED FROM PYTHON SOURCE LINES 31-33 Setup ----- .. GENERATED FROM PYTHON SOURCE LINES 33-45 .. code-block:: Python # Import packages import pandas as pd import matplotlib.pyplot as plt import pydmr import dcmri as dc # Fetch the data from the TRISTAN rifampicin study: dmrfile = dc.fetch('tristan_humans_patients_rifampicin') data = pydmr.read(dmrfile, 'nest') rois, pars = data['rois'], data['pars'] .. GENERATED FROM PYTHON SOURCE LINES 46-50 Model definition ---------------- In order to avoid some repetition in this script, we define a function that returns a trained model for a single dataset with 2 scans: .. GENERATED FROM PYTHON SOURCE LINES 50-97 .. code-block:: Python def tristan_human_2scan(roi, par, **kwargs): model = dc.AortaLiver2scan( # Injection parameters weight = par['weight'], agent = 'gadoxetate', dose = par['dose_1'], dose2 = par['dose_2'], rate = 1, # Acquisition parameters field_strength = 3, t0 = par['t0'], TR = par['TR'], FA = par['FA_1'], FA2 = par['FA_2'], TS = roi['time_1'][1]-roi['time_1'][0], # Signal parameters R10a = 1/par['T1_aorta_1'], R10l = 1/par['T1_liver_1'], R102a = 1/par['T1_aorta_3'], R102l = 1/par['T1_liver_3'], # Tissue parameters vol = par['liver_volume'], ) xdata = ( roi['time_1'][roi['aorta_1_accept']] - roi['time_1'][0], roi['time_2'][roi['aorta_2_accept']] - roi['time_1'][0], roi['time_1'][roi['liver_1_accept']] - roi['time_1'][0], roi['time_2'][roi['liver_2_accept']] - roi['time_1'][0], ) ydata = ( roi['aorta_1'][roi['aorta_1_accept']], roi['aorta_2'][roi['aorta_2_accept']], roi['liver_1'][roi['liver_1_accept']], roi['liver_2'][roi['liver_2_accept']], ) model.train(xdata, ydata, **kwargs) return xdata, ydata, model .. GENERATED FROM PYTHON SOURCE LINES 98-101 Before running the full analysis on all cases, lets illustrate the results by fitting the baseline visit for the first subject. We use maximum verbosity to get some feedback about the iterations: .. GENERATED FROM PYTHON SOURCE LINES 101-109 .. code-block:: Python xdata, ydata, model = tristan_human_2scan( rois['001']['control'], pars['001']['control'], xtol=1e-3, verbose=2, ) .. rst-class:: sphx-glr-script-out .. code-block:: none Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 1.2841e+15 2.82e+17 1 2 3.1276e+14 9.71e+14 3.15e+06 2.17e+17 2 3 1.3675e+14 1.76e+14 4.61e+06 1.67e+17 3 4 7.9008e+13 5.77e+13 4.37e+06 1.03e+17 4 5 5.8651e+13 2.04e+13 1.38e+06 1.25e+17 5 6 4.1743e+13 1.69e+13 2.89e+05 1.09e+17 6 7 3.1627e+13 1.01e+13 1.24e+04 7.94e+16 `xtol` termination condition is satisfied. Function evaluations 7, initial cost 1.2841e+15, final cost 3.1627e+13, first-order optimality 7.94e+16. Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 3.1152e+14 5.45e+14 1 2 6.4619e+13 2.47e+14 2.66e+06 1.24e+14 2 3 1.6642e+13 4.80e+13 9.88e+03 1.06e+14 `xtol` termination condition is satisfied. Function evaluations 3, initial cost 3.1152e+14, final cost 1.6642e+13, first-order optimality 1.06e+14. Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 4.8270e+13 7.97e+16 1 2 2.8963e+13 1.93e+13 1.09e+07 5.62e+16 2 3 2.4603e+13 4.36e+12 1.88e+06 6.19e+16 3 4 2.3178e+13 1.42e+12 3.57e+05 5.34e+16 4 5 2.2740e+13 4.38e+11 5.83e+04 4.61e+16 `xtol` termination condition is satisfied. Function evaluations 5, initial cost 4.8270e+13, final cost 2.2740e+13, first-order optimality 4.61e+16. .. GENERATED FROM PYTHON SOURCE LINES 110-112 Plot the results to check that the model has fitted the data. The plot also shows the concentration in the two liver compartments separately: .. GENERATED FROM PYTHON SOURCE LINES 112-115 .. code-block:: Python model.plot(xdata, ydata) .. image-sg:: /examples/liver/images/sphx_glr_plot_tristan_patients_001.png :alt: plot tristan patients :srcset: /examples/liver/images/sphx_glr_plot_tristan_patients_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 116-119 Print the measured model parameters and any derived parameters. Standard deviations are included as a measure of parameter uncertainty, indicate that all parameters are identified robustly: .. GENERATED FROM PYTHON SOURCE LINES 119-122 .. code-block:: Python model.print_params(round_to=3) .. rst-class:: sphx-glr-script-out .. code-block:: none -------------------------------- Free parameters with their stdev -------------------------------- Aorta second signal scale factor (S02a): 163286585.61 (263658.446) a.u. Liver second signal scale factor (S02l): 107959241.632 (944770.548) a.u. Second bolus arrival time (BAT2): 7641.273 (0.443) sec First bolus arrival time (BAT): 76.792 (0.435) sec Cardiac output (CO): 172.573 (2.078) mL/sec Heart-lung mean transit time (Thl): 15.818 (0.571) sec Heart-lung dispersion (Dhl): 0.473 (0.009) Organs blood mean transit time (To): 30.691 (0.83) sec Organs extraction fraction (Eo): 0.172 (0.005) Organs extravascular mean transit time (Toe): 270.994 (19.275) sec Body extraction fraction (Eb): 0.044 (0.003) Liver extracellular volume fraction (ve): 0.2 (0.012) mL/cm3 Extracellular mean transit time (Te): 54.082 (4.59) sec Extracellular dispersion (De): 0.831 (0.026) Initial hepatocellular uptake rate (khe_i): 0.0 (0.0) mL/sec/cm3 Final hepatocellular uptake rate (khe_f): 0.0 (0.0) mL/sec/cm3 Initial hepatocellular mean transit time (Th_i): 926.384 (385.901) sec Final hepatocellular mean transit time (Th_f): 1517.281 (1841.527) sec ---------------------------- Fixed and derived parameters ---------------------------- Hematocrit (H): 0.45 Hepatocellular mean transit time (Th): 1221.832 sec Hepatocellular uptake rate (khe): 0.0 mL/sec/cm3 Biliary tissue excretion rate (Kbh): 0.001 mL/sec/cm3 Hepatocellular tissue uptake rate (Khe): 0.002 mL/sec/cm3 Biliary excretion rate (kbh): 0.001 mL/sec/cm3 Initial biliary excretion rate (kbh_i): 0.001 mL/sec/cm3 Final biliary excretion rate (kbh_f): 0.001 mL/sec/cm3 Liver blood clearance (CL): 0.35 mL/sec .. GENERATED FROM PYTHON SOURCE LINES 123-129 Fit all data ------------ Now that we have illustrated an individual result in some detail, we proceed with fitting the data for all 3 patients, at baseline and rifampicin visit. We do not print output for these individual computations and instead store results in one single dataframe: .. GENERATED FROM PYTHON SOURCE LINES 129-160 .. code-block:: Python results = [] # Loop over all datasets for subj in rois.keys(): for visit in rois[subj].keys(): roi = rois[subj][visit] par = pars[subj][visit] # Generate a trained model for the scan: _, _, model = tristan_human_2scan(roi, par, xtol=1e-3) # Export fitted parameters as lists rows = model.export_params(type='list') # Add visit and subject info rows = [row + [visit, subj] for row in rows] # Add to the list of all results results += rows # Combine all results into a single dataframe. cols = ['parameter', 'name', 'value', 'unit', 'stdev', 'visit', 'subject'] results = pd.DataFrame(results, columns=cols) # Print all results print(results.to_string()) .. rst-class:: sphx-glr-script-out .. code-block:: none parameter name value unit stdev visit subject 0 S02a Aorta second signal scale factor 1.632866e+08 a.u. 2.636584e+05 control 001 1 S02l Liver second signal scale factor 1.079592e+08 a.u. 9.447705e+05 control 001 2 BAT2 Second bolus arrival time 7.641273e+03 sec 4.432600e-01 control 001 3 BAT First bolus arrival time 7.679155e+01 sec 4.350714e-01 control 001 4 CO Cardiac output 1.725733e+02 mL/sec 2.077570e+00 control 001 5 Thl Heart-lung mean transit time 1.581789e+01 sec 5.711453e-01 control 001 6 Dhl Heart-lung dispersion 4.728497e-01 8.677433e-03 control 001 7 To Organs blood mean transit time 3.069064e+01 sec 8.304487e-01 control 001 8 Eo Organs extraction fraction 1.715850e-01 5.219545e-03 control 001 9 Toe Organs extravascular mean transit time 2.709938e+02 sec 1.927540e+01 control 001 10 Eb Body extraction fraction 4.375584e-02 2.869370e-03 control 001 11 H Hematocrit 4.500000e-01 0.000000e+00 control 001 12 ve Liver extracellular volume fraction 1.998686e-01 mL/cm3 1.190225e-02 control 001 13 Te Extracellular mean transit time 5.408241e+01 sec 4.589613e+00 control 001 14 De Extracellular dispersion 8.312908e-01 2.604401e-02 control 001 15 khe_i Initial hepatocellular uptake rate 4.820300e-04 mL/sec/cm3 1.010929e-04 control 001 16 khe_f Final hepatocellular uptake rate 3.622122e-04 mL/sec/cm3 8.886465e-05 control 001 17 Th_i Initial hepatocellular mean transit time 9.263840e+02 sec 3.859014e+02 control 001 18 Th_f Final hepatocellular mean transit time 1.517281e+03 sec 1.841527e+03 control 001 19 Th Hepatocellular mean transit time 1.221832e+03 sec 0.000000e+00 control 001 20 khe Hepatocellular uptake rate 4.221211e-04 mL/sec/cm3 0.000000e+00 control 001 21 Kbh Biliary tissue excretion rate 8.184429e-04 mL/sec/cm3 0.000000e+00 control 001 22 Khe Hepatocellular tissue uptake rate 2.111993e-03 mL/sec/cm3 0.000000e+00 control 001 23 kbh Biliary excretion rate 6.548618e-04 mL/sec/cm3 0.000000e+00 control 001 24 kbh_i Initial biliary excretion rate 8.637146e-04 mL/sec/cm3 0.000000e+00 control 001 25 kbh_f Final biliary excretion rate 5.273457e-04 mL/sec/cm3 0.000000e+00 control 001 26 CL Liver blood clearance 3.500209e-01 mL/sec 0.000000e+00 control 001 27 S02a Aorta second signal scale factor 1.328103e+08 a.u. 5.846473e+05 drug 001 28 S02l Liver second signal scale factor 9.688988e+07 a.u. 9.548153e+05 drug 001 29 BAT2 Second bolus arrival time 6.904645e+03 sec 1.710079e-01 drug 001 30 BAT First bolus arrival time 7.979890e+01 sec 1.687411e-01 drug 001 31 CO Cardiac output 1.721139e+02 mL/sec 3.152113e+00 drug 001 32 Thl Heart-lung mean transit time 8.264760e+00 sec 2.712979e-01 drug 001 33 Dhl Heart-lung dispersion 5.218754e-01 1.019463e-02 drug 001 34 To Organs blood mean transit time 2.752833e+01 sec 9.750224e-01 drug 001 35 Eo Organs extraction fraction 1.222519e-01 5.434559e-03 drug 001 36 Toe Organs extravascular mean transit time 3.209690e+02 sec 2.949666e+01 drug 001 37 Eb Body extraction fraction 2.789956e-02 2.807268e-03 drug 001 38 H Hematocrit 4.500000e-01 0.000000e+00 drug 001 39 ve Liver extracellular volume fraction 1.421242e-01 mL/cm3 1.574084e-02 drug 001 40 Te Extracellular mean transit time 4.783043e+01 sec 7.656008e+00 drug 001 41 De Extracellular dispersion 7.576965e-01 5.673443e-02 drug 001 42 khe_i Initial hepatocellular uptake rate 5.044245e-04 mL/sec/cm3 1.387541e-04 drug 001 43 khe_f Final hepatocellular uptake rate 5.822585e-04 mL/sec/cm3 1.616184e-04 drug 001 44 Th_i Initial hepatocellular mean transit time 8.043769e+02 sec 3.424670e+02 drug 001 45 Th_f Final hepatocellular mean transit time 9.579056e+02 sec 8.400133e+02 drug 001 46 Th Hepatocellular mean transit time 8.811412e+02 sec 0.000000e+00 drug 001 47 khe Hepatocellular uptake rate 5.433415e-04 mL/sec/cm3 0.000000e+00 drug 001 48 Kbh Biliary tissue excretion rate 1.134892e-03 mL/sec/cm3 0.000000e+00 drug 001 49 Khe Hepatocellular tissue uptake rate 3.823005e-03 mL/sec/cm3 0.000000e+00 drug 001 50 kbh Biliary excretion rate 9.735963e-04 mL/sec/cm3 0.000000e+00 drug 001 51 kbh_i Initial biliary excretion rate 1.066510e-03 mL/sec/cm3 0.000000e+00 drug 001 52 kbh_f Final biliary excretion rate 8.955745e-04 mL/sec/cm3 0.000000e+00 drug 001 53 CL Liver blood clearance 4.750073e-01 mL/sec 0.000000e+00 drug 001 54 S02a Aorta second signal scale factor 1.882574e+08 a.u. 1.691088e+06 control 002 55 S02l Liver second signal scale factor 7.844688e+07 a.u. 2.974411e+06 control 002 56 BAT2 Second bolus arrival time 7.585136e+03 sec 8.029937e-01 control 002 57 BAT First bolus arrival time 8.501632e+01 sec 8.290006e-01 control 002 58 CO Cardiac output 1.758135e+02 mL/sec 3.654334e+00 control 002 59 Thl Heart-lung mean transit time 1.666173e+01 sec 1.033130e+00 control 002 60 Dhl Heart-lung dispersion 5.146619e-01 1.861645e-02 control 002 61 To Organs blood mean transit time 3.171744e+01 sec 1.038976e+00 control 002 62 Eo Organs extraction fraction 1.859614e-01 5.589371e-03 control 002 63 Toe Organs extravascular mean transit time 6.509501e+02 sec 3.903126e+01 control 002 64 Eb Body extraction fraction 1.193749e-02 3.665511e-03 control 002 65 H Hematocrit 4.500000e-01 0.000000e+00 control 002 66 ve Liver extracellular volume fraction 3.896929e-01 mL/cm3 2.920617e-02 control 002 67 Te Extracellular mean transit time 4.337504e+01 sec 4.792783e+00 control 002 68 De Extracellular dispersion 8.058836e-01 3.688731e-02 control 002 69 khe_i Initial hepatocellular uptake rate 2.460186e-03 mL/sec/cm3 4.084303e-04 control 002 70 khe_f Final hepatocellular uptake rate 2.120268e-03 mL/sec/cm3 1.474294e-04 control 002 71 Th_i Initial hepatocellular mean transit time 6.029080e+02 sec 7.314390e+02 control 002 72 Th_f Final hepatocellular mean transit time 1.383018e+04 sec 4.816187e+03 control 002 73 Th Hepatocellular mean transit time 7.216545e+03 sec 0.000000e+00 control 002 74 khe Hepatocellular uptake rate 2.290227e-03 mL/sec/cm3 0.000000e+00 control 002 75 Kbh Biliary tissue excretion rate 1.385705e-04 mL/sec/cm3 0.000000e+00 control 002 76 Khe Hepatocellular tissue uptake rate 5.877005e-03 mL/sec/cm3 0.000000e+00 control 002 77 kbh Biliary excretion rate 8.457055e-05 mL/sec/cm3 0.000000e+00 control 002 78 kbh_i Initial biliary excretion rate 1.012272e-03 mL/sec/cm3 0.000000e+00 control 002 79 kbh_f Final biliary excretion rate 4.412864e-05 mL/sec/cm3 0.000000e+00 control 002 80 CL Liver blood clearance 2.929624e+00 mL/sec 0.000000e+00 control 002 81 S02a Aorta second signal scale factor 1.662998e+08 a.u. 4.315369e+05 drug 002 82 S02l Liver second signal scale factor 1.039724e+08 a.u. 3.938801e+06 drug 002 83 BAT2 Second bolus arrival time 7.040979e+03 sec 1.800162e-01 drug 002 84 BAT First bolus arrival time 7.460534e+01 sec 1.854488e-01 drug 002 85 CO Cardiac output 1.419702e+02 mL/sec 1.934519e+00 drug 002 86 Thl Heart-lung mean transit time 2.146588e+01 sec 2.643157e-01 drug 002 87 Dhl Heart-lung dispersion 3.913142e-01 6.718867e-03 drug 002 88 To Organs blood mean transit time 2.214418e+01 sec 1.215683e+00 drug 002 89 Eo Organs extraction fraction 2.077079e-01 1.116015e-02 drug 002 90 Toe Organs extravascular mean transit time 1.860298e+02 sec 1.863163e+01 drug 002 91 Eb Body extraction fraction 8.817654e-02 3.672526e-03 drug 002 92 H Hematocrit 4.500000e-01 0.000000e+00 drug 002 93 ve Liver extracellular volume fraction 2.040219e-01 mL/cm3 1.953743e-02 drug 002 94 Te Extracellular mean transit time 4.962744e+01 sec 6.220009e+00 drug 002 95 De Extracellular dispersion 7.524833e-01 4.927369e-02 drug 002 96 khe_i Initial hepatocellular uptake rate 9.605064e-04 mL/sec/cm3 8.933224e-05 drug 002 97 khe_f Final hepatocellular uptake rate 2.666436e-03 mL/sec/cm3 2.504474e-04 drug 002 98 Th_i Initial hepatocellular mean transit time 9.437895e+03 sec 7.435618e+03 drug 002 99 Th_f Final hepatocellular mean transit time 9.924794e+02 sec 3.095791e+02 drug 002 100 Th Hepatocellular mean transit time 5.215187e+03 sec 0.000000e+00 drug 002 101 khe Hepatocellular uptake rate 1.813471e-03 mL/sec/cm3 0.000000e+00 drug 002 102 Kbh Biliary tissue excretion rate 1.917477e-04 mL/sec/cm3 0.000000e+00 drug 002 103 Khe Hepatocellular tissue uptake rate 8.888609e-03 mL/sec/cm3 0.000000e+00 drug 002 104 kbh Biliary excretion rate 1.526269e-04 mL/sec/cm3 0.000000e+00 drug 002 105 kbh_i Initial biliary excretion rate 8.433852e-05 mL/sec/cm3 0.000000e+00 drug 002 106 kbh_f Final biliary excretion rate 8.020096e-04 mL/sec/cm3 0.000000e+00 drug 002 107 CL Liver blood clearance 2.563188e+00 mL/sec 0.000000e+00 drug 002 108 S02a Aorta second signal scale factor 1.862461e+08 a.u. 3.712136e+05 control 003 109 S02l Liver second signal scale factor 1.250913e+08 a.u. 6.908284e+05 control 003 110 BAT2 Second bolus arrival time 6.850662e+03 sec 1.501683e-01 control 003 111 BAT First bolus arrival time 7.028508e+01 sec 1.266807e-01 control 003 112 CO Cardiac output 1.482700e+02 mL/sec 1.456552e+00 control 003 113 Thl Heart-lung mean transit time 1.250971e+01 sec 1.579453e-01 control 003 114 Dhl Heart-lung dispersion 2.833172e-01 2.891299e-03 control 003 115 To Organs blood mean transit time 3.126957e+01 sec 9.019442e-01 control 003 116 Eo Organs extraction fraction 1.749912e-01 7.080471e-03 control 003 117 Toe Organs extravascular mean transit time 2.266253e+02 sec 1.933431e+01 control 003 118 Eb Body extraction fraction 7.161903e-02 2.944341e-03 control 003 119 H Hematocrit 4.500000e-01 0.000000e+00 control 003 120 ve Liver extracellular volume fraction 3.274133e-01 mL/cm3 1.735971e-02 control 003 121 Te Extracellular mean transit time 5.979239e+01 sec 4.391825e+00 control 003 122 De Extracellular dispersion 9.008297e-01 1.336760e-02 control 003 123 khe_i Initial hepatocellular uptake rate 1.107121e-03 mL/sec/cm3 9.981758e-05 control 003 124 khe_f Final hepatocellular uptake rate 3.091978e-03 mL/sec/cm3 1.516869e-04 control 003 125 Th_i Initial hepatocellular mean transit time 2.434978e+03 sec 6.620161e+02 control 003 126 Th_f Final hepatocellular mean transit time 6.003804e+02 sec 7.102712e+01 control 003 127 Th Hepatocellular mean transit time 1.517679e+03 sec 0.000000e+00 control 003 128 khe Hepatocellular uptake rate 2.099549e-03 mL/sec/cm3 0.000000e+00 control 003 129 Kbh Biliary tissue excretion rate 6.589009e-04 mL/sec/cm3 0.000000e+00 control 003 130 Khe Hepatocellular tissue uptake rate 6.412536e-03 mL/sec/cm3 0.000000e+00 control 003 131 kbh Biliary excretion rate 4.431680e-04 mL/sec/cm3 0.000000e+00 control 003 132 kbh_i Initial biliary excretion rate 2.762189e-04 mL/sec/cm3 0.000000e+00 control 003 133 kbh_f Final biliary excretion rate 1.120268e-03 mL/sec/cm3 0.000000e+00 control 003 134 CL Liver blood clearance 2.090544e+00 mL/sec 0.000000e+00 control 003 135 S02a Aorta second signal scale factor 2.054986e+08 a.u. 5.597670e+05 drug 003 136 S02l Liver second signal scale factor 1.278214e+08 a.u. 4.813088e+05 drug 003 137 BAT2 Second bolus arrival time 7.323074e+03 sec 1.454085e-01 drug 003 138 BAT First bolus arrival time 6.827140e+01 sec 1.530142e-01 drug 003 139 CO Cardiac output 1.889740e+02 mL/sec 3.093162e+00 drug 003 140 Thl Heart-lung mean transit time 1.433676e+01 sec 2.500115e-01 drug 003 141 Dhl Heart-lung dispersion 3.813946e-01 7.301855e-03 drug 003 142 To Organs blood mean transit time 2.093434e+01 sec 1.092181e+00 drug 003 143 Eo Organs extraction fraction 1.660923e-01 1.017878e-02 drug 003 144 Toe Organs extravascular mean transit time 1.871734e+02 sec 1.960309e+01 drug 003 145 Eb Body extraction fraction 3.293534e-02 2.653356e-03 drug 003 146 H Hematocrit 4.500000e-01 0.000000e+00 drug 003 147 ve Liver extracellular volume fraction 2.623260e-01 mL/cm3 2.812384e-02 drug 003 148 Te Extracellular mean transit time 5.991617e+01 sec 9.896264e+00 drug 003 149 De Extracellular dispersion 8.822647e-01 3.928749e-02 drug 003 150 khe_i Initial hepatocellular uptake rate 4.189590e-04 mL/sec/cm3 2.469740e-04 drug 003 151 khe_f Final hepatocellular uptake rate 2.710768e-04 mL/sec/cm3 3.335262e-04 drug 003 152 Th_i Initial hepatocellular mean transit time 6.816298e+02 sec 5.081504e+02 drug 003 153 Th_f Final hepatocellular mean transit time 7.154843e+02 sec 1.738251e+03 drug 003 154 Th Hepatocellular mean transit time 6.985571e+02 sec 0.000000e+00 drug 003 155 khe Hepatocellular uptake rate 3.450179e-04 mL/sec/cm3 0.000000e+00 drug 003 156 Kbh Biliary tissue excretion rate 1.431522e-03 mL/sec/cm3 0.000000e+00 drug 003 157 Khe Hepatocellular tissue uptake rate 1.315226e-03 mL/sec/cm3 0.000000e+00 drug 003 158 kbh Biliary excretion rate 1.055997e-03 mL/sec/cm3 0.000000e+00 drug 003 159 kbh_i Initial biliary excretion rate 1.082221e-03 mL/sec/cm3 0.000000e+00 drug 003 160 kbh_f Final biliary excretion rate 1.031013e-03 mL/sec/cm3 0.000000e+00 drug 003 161 CL Liver blood clearance 3.490520e-01 mL/sec 0.000000e+00 drug 003 .. GENERATED FROM PYTHON SOURCE LINES 161-166 Plot individual results ----------------------- Now lets visualise the main results from the study by plotting the drug effect for all volunteers, and for both biomarkers: uptake rate ``khe`` and excretion rate ``kbh``: .. GENERATED FROM PYTHON SOURCE LINES 166-206 .. code-block:: Python # Set up the figure clr = ['tab:blue', 'tab:orange', 'tab:green', 'tab:red', 'tab:purple', 'tab:brown', 'tab:pink', 'tab:gray', 'tab:olive', 'tab:cyan'] fs = 10 fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(8,3)) fig.subplots_adjust(wspace=0.5) ax1.set_title('Hepatocellular uptake rate', fontsize=fs, pad=10) ax1.set_ylabel('khe (mL/min/100mL)', fontsize=fs) ax1.set_ylim(0, 60) ax1.tick_params(axis='x', labelsize=fs) ax1.tick_params(axis='y', labelsize=fs) ax2.set_title('Biliary excretion rate', fontsize=fs, pad=10) ax2.set_ylabel('kbh (mL/min/100mL)', fontsize=fs) ax2.set_ylim(0, 10) ax2.tick_params(axis='x', labelsize=fs) ax2.tick_params(axis='y', labelsize=fs) # Pivot data for both visits to wide format for easy access: v1 = pd.pivot_table(results[results.visit=='control'], values='value', columns='parameter', index='subject') v2 = pd.pivot_table(results[results.visit=='drug'], values='value', columns='parameter', index='subject') # Plot the rate constants in units of mL/min/100mL for s in v1.index: x = ['control'] khe = [6000*v1.at[s,'khe']] kbh = [6000*v1.at[s,'kbh']] if s in v2.index: x += ['drug'] khe += [6000*v2.at[s,'khe']] kbh += [6000*v2.at[s,'kbh']] color = clr[int(s)-1] ax1.plot(x, khe, '-', label=s, marker='o', markersize=6, color=color) ax2.plot(x, kbh, '-', label=s, marker='o', markersize=6, color=color) plt.show() # Choose the last image as a thumbnail for the gallery # sphinx_gallery_thumbnail_number = -1 .. image-sg:: /examples/liver/images/sphx_glr_plot_tristan_patients_002.png :alt: Hepatocellular uptake rate, Biliary excretion rate :srcset: /examples/liver/images/sphx_glr_plot_tristan_patients_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** (6 minutes 50.949 seconds) .. _sphx_glr_download_examples_liver_plot_tristan_patients.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_tristan_patients.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_tristan_patients.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_tristan_patients.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_