..

doc/example/example_visualization.ipynb

@@ -23,7 +23,6 @@
     "from pathlib import Path\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
-    "from IPython.display import display\n",
     "\n",
     "import petab\n",
     "from petab import Problem\n",
@@ -38,7 +37,6 @@
     "# we change some settings to make the plots better readable\n",
     "petab.visualize.plotting.DEFAULT_FIGSIZE[:] = (10, 8)\n",
     "plt.rcParams[\"figure.figsize\"] = petab.visualize.plotting.DEFAULT_FIGSIZE\n",
-    "\n",
     "plt.rcParams[\"font.size\"] = 12\n",
     "plt.rcParams[\"figure.dpi\"] = 150\n",
     "plt.rcParams[\"legend.fontsize\"] = 10"
@@ -90,7 +88,7 @@
     "### Subplots / subsetting the data\n",
     "\n",
     "Measurements or simulations can be grouped by observables, simulation conditions, or datasetIds with the `plot_problem()` function. This can be specified by setting the value of `group_by` parameter to `'observable'` (default), `'simulation'`, or `'dataset'` and by providing corresponding ids in `grouping_list`, which is a list of lists. Each sublist specifies a separate plot and its elements are either simulation condition IDs or observable IDs or the dataset IDs.\n",
-    " \n",
+    "\n",
     "#### By observable\n",
     "\n",
     "We can specify how many subplots there should be and what should be plotted on each of them. It can easily be done by providing `grouping_list`, which by default specifies, which observables should be plotted on a particular plot. The value of `grouping_list` should be a list of lists, each sublist corresponds to a separate plot."
@@ -199,7 +197,7 @@
    "source": [
     "### Plotting simulations\n",
     "\n",
-    "We can also plot simulations together with the meausurements, for example, to judge the model fit. For this, we need to provide a simulation file as `simulations_df`. A simulation file has the same format as the measurement file, but instead of the `measurement` column, it contains simulation outputs in the `simulation` column.\n"
+    "We can also plot simulations together with the meausurements, for example, to judge the model fit. For this, we need to provide a simulation file as `simulations_df`. A simulation file has the same format as the measurement file, but instead of the `measurement` column, it contains simulation outputs in the `simulation` column. The simulations are plotted as solid lines, while the measurements are plotted as dashed lines:"
    ],
    "metadata": {
     "collapsed": false
@@ -335,7 +333,7 @@
     "petab_problem.visualization_df = petab.get_visualization_df(\n",
     "    example_dir_fujita / \"visuSpecs\" / \"Fujita_visuSpec_1.tsv\"\n",
     ")\n",
-    "display(petab_problem.visualization_df)"
+    "petab_problem.visualization_df"
    ],
    "metadata": {
     "collapsed": false