.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "generated\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_generated_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 33-42 .. code-block:: Python # Import packages import pandas as pd import matplotlib.pyplot as plt import dcmri as dc # Fetch the data from the TRISTAN rifampicin study: data = dc.fetch('tristan_gothenburg') .. GENERATED FROM PYTHON SOURCE LINES 43-47 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 47-93 .. code-block:: Python def tristan_human_2scan(data, **kwargs): model = dc.AortaLiver2scan( # Injection parameters weight = data['weight'], agent = data['agent'], dose = data['dose'][0], dose2 = data['dose'][1], rate = data['rate'], # Acquisition parameters field_strength = data['field_strength'], t0 = data['t0'], TR = data['TR'], FA = data['FA'], # Signal parameters R10a = data['R10b'], R102a = data['R102b'], R10l = data['R10l'], R102l = data['R102l'], # Tissue parameters H = data['Hct'], vol = data['vol'], ) xdata = ( data['time1aorta'], data['time2aorta'], data['time1liver'], data['time2liver'], ) ydata = ( data['signal1aorta'], data['signal2aorta'], data['signal1liver'], data['signal2liver'], ) model.train(xdata, ydata, **kwargs) return xdata, ydata, model .. GENERATED FROM PYTHON SOURCE LINES 94-97 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 97-100 .. code-block:: Python xdata, ydata, model = tristan_human_2scan(data[0], 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 1.8931e+15 2.87e+17 1 2 5.2215e+14 1.37e+15 6.96e+06 4.71e+17 2 3 1.9291e+14 3.29e+14 5.60e+06 1.88e+17 3 4 1.1164e+14 8.13e+13 7.47e+06 8.18e+16 4 5 8.1816e+13 2.98e+13 3.02e+06 1.03e+17 5 6 5.8094e+13 2.37e+13 1.36e+05 1.63e+17 `xtol` termination condition is satisfied. Function evaluations 6, initial cost 1.8931e+15, final cost 5.8094e+13, first-order optimality 1.63e+17. Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 3.3436e+14 5.37e+14 1 2 7.6468e+13 2.58e+14 5.54e+06 1.30e+14 2 3 2.8660e+13 4.78e+13 1.07e+04 7.03e+13 `xtol` termination condition is satisfied. Function evaluations 3, initial cost 3.3436e+14, final cost 2.8660e+13, first-order optimality 7.03e+13. Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 8.6754e+13 1.63e+17 1 2 6.0975e+13 2.58e+13 9.44e+06 8.62e+16 2 3 5.3686e+13 7.29e+12 7.06e+05 1.44e+16 3 5 5.3686e+13 0.00e+00 0.00e+00 1.44e+16 `xtol` termination condition is satisfied. Function evaluations 5, initial cost 8.6754e+13, final cost 5.3686e+13, first-order optimality 1.44e+16. .. GENERATED FROM PYTHON SOURCE LINES 101-103 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 103-106 .. code-block:: Python model.plot(xdata, ydata) .. image-sg:: /generated/examples/liver/images/sphx_glr_plot_tristan_patients_001.png :alt: plot tristan patients :srcset: /generated/examples/liver/images/sphx_glr_plot_tristan_patients_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 107-110 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 110-113 .. 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): 199242357.488 (498013.539) a.u. Liver second signal scale factor (S02l): 127994807.149 (754161.353) a.u. Second bolus arrival time (BAT2): 7640.635 (0.23) sec First bolus arrival time (BAT): 75.837 (0.227) sec Cardiac output (CO): 208.349 (2.916) mL/sec Heart-lung mean transit time (Thl): 17.215 (0.311) sec Heart-lung dispersion (Dhl): 0.442 (0.008) Organs blood mean transit time (To): 22.575 (0.985) sec Organs extraction fraction (Eo): 0.168 (0.007) Organs extravascular mean transit time (Toe): 244.098 (23.262) sec Body extraction fraction (Eb): 0.04 (0.003) Liver extracellular volume fraction (ve): 0.156 (0.015) mL/cm3 Extracellular mean transit time (Te): 35.613 (5.478) sec Extracellular dispersion (De): 0.787 (0.059) Initial hepatocellular uptake rate (khe_i): 0.001 (0.0) mL/sec/cm3 Final hepatocellular uptake rate (khe_f): 0.001 (0.0) mL/sec/cm3 Initial hepatocellular mean transit time (Th_i): 911.225 (335.541) sec Final hepatocellular mean transit time (Th_f): 1161.939 (1031.816) sec ---------------------------- Fixed and derived parameters ---------------------------- Hematocrit (H): 0.45 Hepatocellular mean transit time (Th): 1036.582 sec Hepatocellular uptake rate (khe): 0.001 mL/sec/cm3 Biliary tissue excretion rate (Kbh): 0.001 mL/sec/cm3 Hepatocellular tissue uptake rate (Khe): 0.005 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): 0.582 mL/sec .. GENERATED FROM PYTHON SOURCE LINES 114-120 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 120-148 .. code-block:: Python results = [] # Loop over all datasets for scan in data: # Generate a trained model for the scan: _, _, model = tristan_human_2scan(scan, xtol=1e-3) # Convert the parameter dictionary to a dataframe pars = model.export_params() pars = pd.DataFrame.from_dict(pars, orient = 'index', columns = ["name", "value", "unit", 'stdev']) pars['parameter'] = pars.index pars['visit'] = scan['visit'] pars['subject'] = scan['subject'] # Add the dataframe to the list of results results.append(pars) # Combine all results into a single dataframe. results = pd.concat(results).reset_index(drop=True) # Print all results print(results.to_string()) .. rst-class:: sphx-glr-script-out .. code-block:: none name value unit stdev parameter visit subject 0 Aorta second signal scale factor 1.992424e+08 a.u. 4.980135e+05 S02a control 001 1 Liver second signal scale factor 1.279948e+08 a.u. 7.541614e+05 S02l control 001 2 Second bolus arrival time 7.640635e+03 sec 2.302443e-01 BAT2 control 001 3 First bolus arrival time 7.583656e+01 sec 2.269671e-01 BAT control 001 4 Cardiac output 2.083493e+02 mL/sec 2.915613e+00 CO control 001 5 Heart-lung mean transit time 1.721467e+01 sec 3.107741e-01 Thl control 001 6 Heart-lung dispersion 4.421340e-01 7.770281e-03 Dhl control 001 7 Organs blood mean transit time 2.257539e+01 sec 9.847605e-01 To control 001 8 Organs extraction fraction 1.678356e-01 7.170859e-03 Eo control 001 9 Organs extravascular mean transit time 2.440985e+02 sec 2.326207e+01 Toe control 001 10 Body extraction fraction 4.022306e-02 3.422418e-03 Eb control 001 11 Hematocrit 4.500000e-01 0.000000e+00 H control 001 12 Liver extracellular volume fraction 1.556820e-01 mL/cm3 1.495657e-02 ve control 001 13 Extracellular mean transit time 3.561343e+01 sec 5.478327e+00 Te control 001 14 Extracellular dispersion 7.871338e-01 5.949972e-02 De control 001 15 Initial hepatocellular uptake rate 7.043189e-04 mL/sec/cm3 1.387267e-04 khe_i control 001 16 Final hepatocellular uptake rate 6.992077e-04 mL/sec/cm3 1.671761e-04 khe_f control 001 17 Initial hepatocellular mean transit time 9.112253e+02 sec 3.355405e+02 Th_i control 001 18 Final hepatocellular mean transit time 1.161939e+03 sec 1.031816e+03 Th_f control 001 19 Hepatocellular mean transit time 1.036582e+03 sec 0.000000e+00 Th control 001 20 Hepatocellular uptake rate 7.017633e-04 mL/sec/cm3 0.000000e+00 khe control 001 21 Biliary tissue excretion rate 9.647089e-04 mL/sec/cm3 0.000000e+00 Kbh control 001 22 Hepatocellular tissue uptake rate 4.507672e-03 mL/sec/cm3 0.000000e+00 Khe control 001 23 Biliary excretion rate 8.145211e-04 mL/sec/cm3 0.000000e+00 kbh control 001 24 Initial biliary excretion rate 9.265743e-04 mL/sec/cm3 0.000000e+00 kbh_i control 001 25 Final biliary excretion rate 7.266458e-04 mL/sec/cm3 0.000000e+00 kbh_f control 001 26 Liver blood clearance 5.818990e-01 mL/sec 0.000000e+00 CL control 001 27 Aorta second signal scale factor 2.403381e+08 a.u. 1.927638e+06 S02a control 002 28 Liver second signal scale factor 1.093829e+08 a.u. 6.345021e+06 S02l control 002 29 Second bolus arrival time 7.580515e+03 sec 6.668222e-01 BAT2 control 002 30 First bolus arrival time 8.028901e+01 sec 8.048596e-01 BAT control 002 31 Cardiac output 1.899930e+02 mL/sec 3.381674e+00 CO control 002 32 Heart-lung mean transit time 2.248593e+01 sec 1.027472e+00 Thl control 002 33 Heart-lung dispersion 4.278589e-01 1.320897e-02 Dhl control 002 34 Organs blood mean transit time 2.479895e+01 sec 1.467220e+00 To control 002 35 Organs extraction fraction 1.783381e-01 7.799905e-03 Eo control 002 36 Organs extravascular mean transit time 4.919636e+02 sec 4.973204e+01 Toe control 002 37 Body extraction fraction 3.181506e-02 7.150850e-03 Eb control 002 38 Hematocrit 4.500000e-01 0.000000e+00 H control 002 39 Liver extracellular volume fraction 3.524859e-01 mL/cm3 3.169676e-02 ve control 002 40 Extracellular mean transit time 3.926668e+01 sec 5.312582e+00 Te control 002 41 Extracellular dispersion 8.030705e-01 4.983339e-02 De control 002 42 Initial hepatocellular uptake rate 2.535043e-03 mL/sec/cm3 3.880098e-04 khe_i control 002 43 Final hepatocellular uptake rate 1.761714e-03 mL/sec/cm3 1.427542e-04 khe_f control 002 44 Initial hepatocellular mean transit time 8.486214e+02 sec 7.878068e+02 Th_i control 002 45 Final hepatocellular mean transit time 9.973917e+03 sec 4.965847e+03 Th_f control 002 46 Hepatocellular mean transit time 5.411269e+03 sec 0.000000e+00 Th control 002 47 Hepatocellular uptake rate 2.148378e-03 mL/sec/cm3 0.000000e+00 khe control 002 48 Biliary tissue excretion rate 1.847995e-04 mL/sec/cm3 0.000000e+00 Kbh control 002 49 Hepatocellular tissue uptake rate 6.094934e-03 mL/sec/cm3 0.000000e+00 Khe control 002 50 Biliary excretion rate 1.196603e-04 mL/sec/cm3 0.000000e+00 kbh control 002 51 Initial biliary excretion rate 7.630188e-04 mL/sec/cm3 0.000000e+00 kbh_i control 002 52 Final biliary excretion rate 6.492075e-05 mL/sec/cm3 0.000000e+00 kbh_f control 002 53 Liver blood clearance 2.748173e+00 mL/sec 0.000000e+00 CL control 002 54 Aorta second signal scale factor 2.267418e+08 a.u. 5.846613e+05 S02a control 003 55 Liver second signal scale factor 1.487343e+08 a.u. 1.235888e+06 S02l control 003 56 Second bolus arrival time 6.852440e+03 sec 6.208581e-01 BAT2 control 003 57 First bolus arrival time 7.232176e+01 sec 5.988455e-01 BAT control 003 58 Cardiac output 1.743725e+02 mL/sec 2.140203e+00 CO control 003 59 Heart-lung mean transit time 1.096090e+01 sec 6.627178e-01 Thl control 003 60 Heart-lung dispersion 3.789489e-01 1.778646e-02 Dhl control 003 61 Organs blood mean transit time 3.195749e+01 sec 1.285467e+00 To control 003 62 Organs extraction fraction 1.397348e-01 8.344810e-03 Eo control 003 63 Organs extravascular mean transit time 2.592389e+02 sec 3.494318e+01 Toe control 003 64 Body extraction fraction 6.328560e-02 4.056266e-03 Eb control 003 65 Hematocrit 4.500000e-01 0.000000e+00 H control 003 66 Liver extracellular volume fraction 3.366765e-01 mL/cm3 2.097851e-02 ve control 003 67 Extracellular mean transit time 5.567088e+01 sec 4.989146e+00 Te control 003 68 Extracellular dispersion 8.911246e-01 1.899964e-02 De control 003 69 Initial hepatocellular uptake rate 1.057429e-03 mL/sec/cm3 1.211856e-04 khe_i control 003 70 Final hepatocellular uptake rate 3.027705e-03 mL/sec/cm3 1.871704e-04 khe_f control 003 71 Initial hepatocellular mean transit time 2.614921e+03 sec 9.578130e+02 Th_i control 003 72 Final hepatocellular mean transit time 6.000000e+02 sec 9.311993e+01 Th_f control 003 73 Hepatocellular mean transit time 1.607460e+03 sec 0.000000e+00 Th control 003 74 Hepatocellular uptake rate 2.042567e-03 mL/sec/cm3 0.000000e+00 khe control 003 75 Biliary tissue excretion rate 6.220993e-04 mL/sec/cm3 0.000000e+00 Kbh control 003 76 Hepatocellular tissue uptake rate 6.066853e-03 mL/sec/cm3 0.000000e+00 Khe control 003 77 Biliary excretion rate 4.126531e-04 mL/sec/cm3 0.000000e+00 kbh control 003 78 Initial biliary excretion rate 2.536687e-04 mL/sec/cm3 0.000000e+00 kbh_i control 003 79 Final biliary excretion rate 1.105539e-03 mL/sec/cm3 0.000000e+00 kbh_f control 003 80 Liver blood clearance 2.033806e+00 mL/sec 0.000000e+00 CL control 003 81 Aorta second signal scale factor 1.619912e+08 a.u. 6.232932e+05 S02a drug 001 82 Liver second signal scale factor 1.147753e+08 a.u. 6.674490e+05 S02l drug 001 83 Second bolus arrival time 6.901073e+03 sec 1.711258e-01 BAT2 drug 001 84 First bolus arrival time 7.625469e+01 sec 1.710004e-01 BAT drug 001 85 Cardiac output 1.911090e+02 mL/sec 3.536017e+00 CO drug 001 86 Heart-lung mean transit time 1.297264e+01 sec 2.857888e-01 Thl drug 001 87 Heart-lung dispersion 4.250882e-01 8.928510e-03 Dhl drug 001 88 Organs blood mean transit time 2.046576e+01 sec 9.933413e-01 To drug 001 89 Organs extraction fraction 1.305558e-01 7.600983e-03 Eo drug 001 90 Organs extravascular mean transit time 2.386942e+02 sec 2.774625e+01 Toe drug 001 91 Body extraction fraction 3.225480e-02 2.969841e-03 Eb drug 001 92 Hematocrit 4.500000e-01 0.000000e+00 H drug 001 93 Liver extracellular volume fraction 1.474575e-01 mL/cm3 1.688086e-02 ve drug 001 94 Extracellular mean transit time 4.452130e+01 sec 7.713305e+00 Te drug 001 95 Extracellular dispersion 7.326356e-01 6.784303e-02 De drug 001 96 Initial hepatocellular uptake rate 4.686835e-04 mL/sec/cm3 1.528837e-04 khe_i drug 001 97 Final hepatocellular uptake rate 5.532236e-04 mL/sec/cm3 2.045911e-04 khe_f drug 001 98 Initial hepatocellular mean transit time 8.188752e+02 sec 4.209293e+02 Th_i drug 001 99 Final hepatocellular mean transit time 8.919273e+02 sec 9.333918e+02 Th_f drug 001 100 Hepatocellular mean transit time 8.554012e+02 sec 0.000000e+00 Th drug 001 101 Hepatocellular uptake rate 5.109535e-04 mL/sec/cm3 0.000000e+00 khe drug 001 102 Biliary tissue excretion rate 1.169042e-03 mL/sec/cm3 0.000000e+00 Kbh drug 001 103 Hepatocellular tissue uptake rate 3.465090e-03 mL/sec/cm3 0.000000e+00 Khe drug 001 104 Biliary excretion rate 9.966581e-04 mL/sec/cm3 0.000000e+00 kbh drug 001 105 Initial biliary excretion rate 1.041114e-03 mL/sec/cm3 0.000000e+00 kbh_i drug 001 106 Final biliary excretion rate 9.558431e-04 mL/sec/cm3 0.000000e+00 kbh_f drug 001 107 Liver blood clearance 4.466927e-01 mL/sec 0.000000e+00 CL drug 001 108 Aorta second signal scale factor 2.013421e+08 a.u. 7.742127e+05 S02a drug 002 109 Liver second signal scale factor 1.289544e+08 a.u. 6.340100e+05 S02l drug 002 110 Second bolus arrival time 7.047597e+03 sec 2.091382e-01 BAT2 drug 002 111 First bolus arrival time 8.128192e+01 sec 2.678799e-01 BAT drug 002 112 Cardiac output 1.910242e+02 mL/sec 4.212239e+00 CO drug 002 113 Heart-lung mean transit time 1.394512e+01 sec 4.404304e-01 Thl drug 002 114 Heart-lung dispersion 4.357685e-01 1.129772e-02 Dhl drug 002 115 Organs blood mean transit time 2.034010e+01 sec 1.484667e+00 To drug 002 116 Organs extraction fraction 1.656891e-01 1.385397e-02 Eo drug 002 117 Organs extravascular mean transit time 1.829893e+02 sec 2.683857e+01 Toe drug 002 118 Body extraction fraction 6.700816e-02 4.154776e-03 Eb drug 002 119 Hematocrit 4.500000e-01 0.000000e+00 H drug 002 120 Liver extracellular volume fraction 1.537814e-01 mL/cm3 3.468108e-02 ve drug 002 121 Extracellular mean transit time 4.124682e+01 sec 1.308810e+01 Te drug 002 122 Extracellular dispersion 7.690209e-01 1.132437e-01 De drug 002 123 Initial hepatocellular uptake rate 1.431656e-03 mL/sec/cm3 2.298980e-04 khe_i drug 002 124 Final hepatocellular uptake rate 2.305792e-03 mL/sec/cm3 3.383085e-04 khe_f drug 002 125 Initial hepatocellular mean transit time 1.469190e+03 sec 5.443912e+02 Th_i drug 002 126 Final hepatocellular mean transit time 9.759390e+02 sec 4.362707e+02 Th_f drug 002 127 Hepatocellular mean transit time 1.222565e+03 sec 0.000000e+00 Th drug 002 128 Hepatocellular uptake rate 1.868724e-03 mL/sec/cm3 0.000000e+00 khe drug 002 129 Biliary tissue excretion rate 8.179527e-04 mL/sec/cm3 0.000000e+00 Kbh drug 002 130 Hepatocellular tissue uptake rate 1.215182e-02 mL/sec/cm3 0.000000e+00 Khe drug 002 131 Biliary excretion rate 6.921668e-04 mL/sec/cm3 0.000000e+00 kbh drug 002 132 Initial biliary excretion rate 5.759762e-04 mL/sec/cm3 0.000000e+00 kbh_i drug 002 133 Final biliary excretion rate 8.670814e-04 mL/sec/cm3 0.000000e+00 kbh_f drug 002 134 Liver blood clearance 2.641283e+00 mL/sec 0.000000e+00 CL drug 002 135 Aorta second signal scale factor 2.461252e+08 a.u. 9.753483e+05 S02a drug 003 136 Liver second signal scale factor 1.516859e+08 a.u. 7.478764e+05 S02l drug 003 137 Second bolus arrival time 7.323665e+03 sec 5.632807e-01 BAT2 drug 003 138 First bolus arrival time 6.847094e+01 sec 7.236456e-01 BAT drug 003 139 Cardiac output 2.102836e+02 mL/sec 6.133358e+00 CO drug 003 140 Heart-lung mean transit time 1.470847e+01 sec 5.725803e-01 Thl drug 003 141 Heart-lung dispersion 3.151611e-01 1.247583e-02 Dhl drug 003 142 Organs blood mean transit time 1.647924e+01 sec 1.283423e+00 To drug 003 143 Organs extraction fraction 1.678818e-01 1.773208e-02 Eo drug 003 144 Organs extravascular mean transit time 1.385754e+02 sec 1.971961e+01 Toe drug 003 145 Body extraction fraction 3.570999e-02 2.687032e-03 Eb drug 003 146 Hematocrit 4.500000e-01 0.000000e+00 H drug 003 147 Liver extracellular volume fraction 2.531379e-01 mL/cm3 3.913259e-02 ve drug 003 148 Extracellular mean transit time 5.787234e+01 sec 1.501888e+01 Te drug 003 149 Extracellular dispersion 9.502423e-01 4.893993e-02 De drug 003 150 Initial hepatocellular uptake rate 4.003029e-04 mL/sec/cm3 3.242286e-04 khe_i drug 003 151 Final hepatocellular uptake rate 2.865731e-04 mL/sec/cm3 4.688460e-04 khe_f drug 003 152 Initial hepatocellular mean transit time 7.608810e+02 sec 8.235358e+02 Th_i drug 003 153 Final hepatocellular mean transit time 7.613988e+02 sec 2.570422e+03 Th_f drug 003 154 Hepatocellular mean transit time 7.611399e+02 sec 0.000000e+00 Th drug 003 155 Hepatocellular uptake rate 3.434380e-04 mL/sec/cm3 0.000000e+00 khe drug 003 156 Biliary tissue excretion rate 1.313819e-03 mL/sec/cm3 0.000000e+00 Kbh drug 003 157 Hepatocellular tissue uptake rate 1.356723e-03 mL/sec/cm3 0.000000e+00 Khe drug 003 158 Biliary excretion rate 9.812416e-04 mL/sec/cm3 0.000000e+00 kbh drug 003 159 Initial biliary excretion rate 9.815754e-04 mL/sec/cm3 0.000000e+00 kbh_i drug 003 160 Final biliary excretion rate 9.809079e-04 mL/sec/cm3 0.000000e+00 kbh_f drug 003 161 Liver blood clearance 3.474537e-01 mL/sec 0.000000e+00 CL drug 003 .. GENERATED FROM PYTHON SOURCE LINES 149-154 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 154-194 .. 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:: /generated/examples/liver/images/sphx_glr_plot_tristan_patients_002.png :alt: Hepatocellular uptake rate, Biliary excretion rate :srcset: /generated/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:** (13 minutes 36.366 seconds) .. _sphx_glr_download_generated_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 `_