added paper plots

Author: ngr-francesco

examples/Frey1998_Tag_Decay.ods

@@ -0,0 +1,21 @@
+axes.labelsize: large
+axes.linewidth: 1.5
+axes.labelpad: 2.0
+axes.spines.right: False
+axes.spines.top: False
+
+xtick.major.size: 5
+xtick.major.width: 1.5
+xtick.labelsize: large
+xtick.direction: out
+
+ytick.major.size: 5
+ytick.major.width: 1.5
+ytick.labelsize: large
+ytick.direction: out
+
+legend.frameon: False
+legend.fontsize: large
+
+figure.frameon: False
+

examples/Simulation_results.ipynb

@@ -4,24 +4,24 @@
 from examples.required_files.const import *
 from virtual_lab.settings import prefs
 with open("experimental_data.json","r") as file:
-    exp_data = json.load(file)
+    STC_data = json.load(file)
 
 # TODO: this looks terrible, I have to implement a better experimental data management system
 data_LTP = {}
-names = [name for name in exp_data if "Matsuzaki" in name]
+names = [name for name in STC_data if "Matsuzaki" in name]
 names.append("renorm_var")
 names.append("time_unit")
 for name in names:
-    data_LTP[name] = exp_data[name]
+    data_LTP[name] = STC_data[name]
 data_LTD = {}   
-names = [name for name in exp_data if "Kasai" in name]
+names = [name for name in STC_data if "Kasai" in name]
 names.append("renorm_var")
 names.append("time_unit")
 T = 2*3600
 
 
 for name in names:
-    data_LTD[name] = exp_data[name]
+    data_LTD[name] = STC_data[name]
 from virtual_lab.model import Model
 def create_experiments(model:Model, **kwargs):
     # Set the global time duration for the experiments

examples/Untitled(1).ipynb

@@ -40,6 +40,7 @@ def set_initial_values(self,stochastic_simulation):
             # This is a bit of a cheat, but I'll check if without this it still works.
             # TODO: check!
             self.nf_0 = np.mean(self.nf)
+        self.variables.Vpsd = 1
         self.variables.V_eff = self.nu*self.nf_0*self.tau_Vd + self.variables.Vpsd 
         self.variables.Vd =  self.eql    * self.variables.V_eff
         self.variables.Vs = (1-self.eql) * self.variables.V_eff

examples/__init__.py

@@ -1,111 +1,139 @@
 {
     "color_coding": {
-        "v": [
-            0.4980392156862745,
-            0.788235294117647,
-            0.4980392156862745
-        ],
-        "u": [
-            0.7450980392156863,
-            0.6823529411764706,
-            0.8313725490196079
-        ],
-        "a_in": [
-            0.9921568627450981,
-            0.7529411764705882,
-            0.5254901960784314
+        "Vd": "#df7c20",
+        "Vs": "#bbce50",
+        "Vpsd": "#a782c9",
+        "V_n": [
+            0.5803921568627451,
+            0.403921568627451,
+            0.7411764705882353,
+            1.0
         ],
-        "spikes": "#1f77b4"
-    },
-    "var": [
-        [
-            1.0,
-            1.0,
-            0.6
+        "V_tot": [
+            0.12156862745098039,
+            0.4666666666666667,
+            0.7058823529411765,
+            1.0
         ],
-        [
-            0.2196078431372549,
-            0.4235294117647059,
-            0.6901960784313725
+        "Ve": [
+            0.5490196078431373,
+            0.33725490196078434,
+            0.29411764705882354,
+            1.0
         ],
-        [
+        "stim": [
             0.9411764705882353,
             0.00784313725490196,
-            0.4980392156862745
+            0.4980392156862745,
+            1.0
         ],
-        [
+        "LFS": [
             0.7490196078431373,
             0.3568627450980392,
-            0.09019607843137253
+            0.09019607843137253,
+            1.0
         ],
-        [
-            0.4,
-            0.4,
-            0.4
+        "xlinkers": [
+            0.9921568627450981,
+            0.7529411764705882,
+            0.5254901960784314,
+            1.0
         ],
-        [
-            0.12156862745098039,
-            0.4666666666666667,
-            0.7058823529411765
+        "protein": [
+            0.7450980392156863,
+            0.6823529411764706,
+            0.8313725490196079,
+            1.0
+        ],
+        "sLTP_Matsuzaki": "#273914",
+        "sLTD_Kasai_Noguchi": "#391414",
+        "Vpsd_ref": "tab:blue",
+        "V_tot_ref": "tab:orange",
+        "V_eff": "#ff4d4d",
+        "crosslink": [
+            0.4980392156862745,
+            0.788235294117647,
+            0.4980392156862745,
+            1.0
         ],
-        [
+        "Matsuzaki 2004": [
             1.0,
             0.4980392156862745,
-            0.054901960784313725
+            0.054901960784313725,
+            1.0
         ],
-        [
+        "Kasai Noguchi 2015": [
             0.17254901960784313,
             0.6274509803921569,
-            0.17254901960784313
+            0.17254901960784313,
+            1.0
         ],
+        "y": "tab:blue",
+        "g": "tab:orange",
+        "my_event": "brown"
+    },
+    "var": [
         [
             0.8392156862745098,
             0.15294117647058825,
-            0.1568627450980392
-        ],
-        [
-            0.5803921568627451,
-            0.403921568627451,
-            0.7411764705882353
-        ],
-        [
-            0.5490196078431373,
-            0.33725490196078434,
-            0.29411764705882354
+            0.1568627450980392,
+            1.0
         ],
         [
             0.8901960784313725,
             0.4666666666666667,
-            0.7607843137254902
+            0.7607843137254902,
+            1.0
         ],
         [
             0.4980392156862745,
             0.4980392156862745,
-            0.4980392156862745
+            0.4980392156862745,
+            1.0
         ],
         [
             0.7372549019607844,
             0.7411764705882353,
-            0.13333333333333333
+            0.13333333333333333,
+            1.0
         ],
         [
             0.09019607843137255,
             0.7450980392156863,
-            0.8117647058823529
-        ]
+            0.8117647058823529,
+            1.0
+        ],
+        [
+            [
+                0.9411764705882353,
+                0.00784313725490196,
+                0.4980392156862745,
+                1.0
+            ]
+        ],
+        "#256f25",
+        "#273914",
+        "#391414"
     ],
     "event": [
-        "#ff7f0e",
-        "#2ca02c",
-        "#d62728",
-        "#9467bd",
-        "#8c564b",
-        "#e377c2",
-        "#7f7f7f",
-        "#bcbd22",
-        "#17becf"
+        [
+            0.2196078431372549,
+            0.4235294117647059,
+            0.6901960784313725,
+            1.0
+        ],
+        [
+            1.0,
+            1.0,
+            0.6,
+            1.0
+        ]
     ],
     "_ordered_quantities": [
-        "spikes"
+        "stim",
+        "LFS",
+        "crosslink",
+        "protein",
+        "my_event"
     ]
 }

examples/fonseca_and_szabo.ipynb

@@ -69,11 +69,19 @@ def add(self, experiments, idx = None):
                 self.experiments.append(experiment)
                 self._exp_names.append(experiment.name)
             else:
-                if not idx in range(len(self.experiments)):
+                if not idx in range(-len(self.experiments),len(self.experiments)):
                     warn(f"Index {idx} is not valid for this class containing"
-                    " {len(self.experiments)} experiments. Will simply append at the end") 
-                self.experiments.insert(idx,experiment)
-                self._exp_names.append(experiment.name)
+                    " {len(self.experiments)} experiments. Will simply append at the end")
+                if idx == -1:
+                    self.experiments.append(experiment)
+                    self._exp_names.append(experiment.name)
+                if idx < -1:
+                    self.experiments.insert(idx+1, experiment)
+                    self._exp_names.insert(idx+1,experiment.name)
+                else:
+                    self.experiments.insert(idx,experiment)
+                    self._exp_names.insert(idx,experiment.name)
+                
 
     def __iter__(self):
         return iter(self.experiments)

examples/paper_plots.ipynb

@@ -402,7 +402,7 @@ def plot_results(self, results = None, exp_names = None,
                 exp = result["experiment"]
                 idx = exp_names.index(result["name"])
                 interval = time_interval[idx] if time_interval is not None else None
-                time_axis,timescale,start,stop,_ = self._get_time_quantities(exp,interval,step,time_unit)
+                time_axis,timescale,start,stop,step = self._get_time_quantities(exp,interval,step,time_unit)
                 values = self.reduce_data(result,start,stop,step)
                 if variables is None:
                     model_variables = self.models[model_name].variables
@@ -745,12 +745,20 @@ def plot_comparison(self, results = None, models = None, exp_names = None, **kwa
             for model in models:
                 results[model] = [self.model_results[model][i].copy() for i in range(len(self.model_results[model]))]
         elif results is not None and isinstance(results,list):
+            tmp = results
             results = {}
-            for result in results:
-                results[result["model"]] = result
+            for result in tmp:
+                try:
+                    results[result['model']]
+                except:
+                    results[result['model']] = []
+                results[result["model"]].append(result)
+        else:
+            print(results)
         result_list = self.sort_results_by_exp(results, exp_names = exp_names)
+        n_cols = kwargs.pop('n_cols', len(results.keys()))
         # Giving exp_names at this point is useless, but I guess it doesn't hurt
-        self.plot_results(result_list,exp_names,n_cols = len(results.keys()), **kwargs)
+        self.plot_results(result_list,exp_names,n_cols =n_cols, **kwargs)
 
     def sort_results_by_exp(self,res_dict, exp_names = None):
         # Not sure if this is necessary but I guess it's a good precaution
@@ -778,9 +786,11 @@ def plot_selected_points(self,results,variables,selection_idx,
                         reference_values = None, reference_data = None, multi_plot = 1,
                         save = True, filename = "img.pdf", **kwargs):
         # TODO: add possibility to plot from multiple results (i.e. a list or dictionary of results like above)
-        # TODO: general thing, implement a figure class which makes it easier to manipulate images without the need to:
-        # 1. Always call these plotting functions with 100 arguments
-        # 2. Always re-plot everything and keep adding functionalities which would be shared among all plots you can do with this package.
+        # TODO: general thing, implement a figure class which makes it easier to manipulate images 
+        #       without the need to:
+        #           1. Always call these plotting functions with 100 arguments
+        #           2. Always re-plot everything and keep adding functionalities which would be 
+        #              shared among all plots you can do with this package.
 
         if not isinstance(results,list):
             if isinstance(results,dict):
@@ -790,12 +800,12 @@ def plot_selected_points(self,results,variables,selection_idx,
         if multi_plot != 1: 
             assert len(results) == multi_plot
             if reference_data is not None:
-                assert len(reference_data) == multi_plot
+                assert len(reference_data) == multi_plot, "Reference data does not cover all the plots requested."
                 multi_data = reference_data
             else:
                 multi_data = [None for k in range(multi_plot)]
             if reference_values is not None:
-                assert len(reference_values) == multi_plot
+                assert len(reference_values) == multi_plot, "Reference values do not cover all the plots requested."
                 multi_values = reference_values
             else:
                 multi_values = [None for k in range(multi_plot)]
@@ -913,15 +923,17 @@ def plot_selected_points(self,results,variables,selection_idx,
                 plot_cols = kwargs.get('n_cols',min(n_plots,4))*multi_plot
                 plot_rows = ceil(n_plots/plot_cols)
                 use_legend = kwargs.get("use_legend", True)
+                title = kwargs.get("title", None)
                 separate_legend = kwargs.get('separate_legend', False)
                 figsize = kwargs.get('figsize',self.prefs.determine_figsize(plot_rows,plot_cols,use_legend,separate_legend))
-                self.logger.debug("Figsize",figsize)
+                self.logger.debug(f"Figsize {figsize}")
                 fontsize = kwargs.get('fontsize',12)
                 plt.rcParams['font.size'] = fontsize
                 fig = plt.figure(figsize=figsize)
                 ax0 = fig.add_subplot(1,multi_plot,1)
                 if multi_plot == 1:
-                    ax0.set_axis_off()
+                    #ax0.set_axis_off()
+                    pass
             else:
                 ax = fig.add_subplot(1, multi_plot, multi_plot_idx+1,sharey = ax0)
             axes = []
@@ -957,7 +969,11 @@ def plot_selected_points(self,results,variables,selection_idx,
                         plt.plot([time_axis[0],time_axis[-1]],[val,val],label = l,ls = "--",lw = 3)
                 plt.xlabel(kwargs.get("xlabel","iterations"))
                 plt.ylabel(kwargs.get('ylabel','ratio of baseline'))
-                plt.title(titles[idx])
+                if title:
+                    title_i = title
+                else:
+                    title_i = titles[idx]
+                plt.title(title_i)
                 # yticks = plt.yticks()[0]
                 #TODO delete!
                 # if multi_plot_idx != 1:
@@ -978,6 +994,8 @@ def plot_selected_points(self,results,variables,selection_idx,
         makedirs(self.prefs.plot_directory[:-1],exist_ok=True)
         fig.savefig(self.prefs.plot_directory + filename)
         plt.show()
+        if kwargs.get('return_data') is True:
+            return points
 
     def determine_label(self,varname):
         if not hasattr(self.model,"labels") or not varname in self.model.labels: