Merge pull request #390 from DiODeProject/issue-389-385-graphics-params

Close #389

docs/MuMoTuserManual.ipynb

@@ -1141,7 +1141,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "##### Advanced options for `SSA`\n",
+    "##### Advanced options for `SSA` and `multiagent`\n",
     "<a id='advoptionsSSA'></a>\n",
     "\n",
     "* `initialState`: proportion of each reactant at timestep zero: remember that the sum of all (non-constant) reactants must be 1.0\n",
@@ -1165,7 +1165,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "##### Advanced options for `multiagent`\n",
+    "##### Advanced options for `multiagent` only\n",
     "<a id='advoptionsmulti'></a>\n",
     "\n",
     "`multiagent` views have all the options described above for the `SSA` simulations and, in addition:\n",
@@ -1176,7 +1176,7 @@
     "  * `barabasi-albert`: Random network with Barabasi-Albert topology. The widgets allow to specify:\n",
     "    * `netParam`: the number of edges every new node (during creation) is linked to\n",
     "  * `dynamic`: Simulation of moving particles in which agent move in a periodic space and interact locally. The widgets allow to specify:\n",
-    "    * `netParam`: range of interaction of the agent\n",
+    "    * `netParam`: range of interaction of the agent (radius)\n",
     "    * `motionCorrelatedness`: motion correlatedness of the agent. Correlatedness = 1 correponds to straight movement, Correlatedness = 0 corresponds to uncorrelated random walk.\n",
     "    * `particleSpeed`: speed of the agent, i.e. displacement in one timestep\n",
     "    * `showTrace`: flag to show the motion trajectory of the agents\n",
@@ -1271,6 +1271,7 @@
     "\n",
     "##### Keyword arguments for `SSA()` and `multiagent()`\n",
     "\n",
+    "- valid for both methods:\n",
     "\n",
     " - `params = None`: list of parameters defined as pairs ('parameter name', value), see [Partial controllers](#partialcont). Rates defaults to `mumot.MuMoTdefault._initialRateValue`, system size defaults to `mumot.MuMoTdefault._systemSize`\n",
     "\n",
@@ -1293,9 +1294,34 @@
     " - `runs = 1`: number of simulation runs to be executed, must be strictly positive\n",
     "\n",
     " - `aggregateResults = True`: aggregate the results from multiple runs, accepts True or False\n",
+    " \n",
+    "  - `legend_fontsize = 14`: specify fontsize of legend (type: integer)\n",
+    "\n",
+    " - `legend_loc = 'upper left'`: specify legend location: combinations like 'upper left', 'lower right', or 'center center' are allowed (9 options in total)\n",
+    "\n",
+    " - `fontsize = None`: specify fontsize for axis-labels, accepts integer, if not given fontsize is automatically derived from length of axis label\n",
+    "\n",
+    " - `xlab = 'time t'`: specify label on x-axis (type: str), if given replaces default\n",
+    "\n",
+    " - `ylab = 'noise correlations'`: specify label on y-axis (type: str), if given replaces default\n",
+    "\n",
+    " - `choose_xrange = None`: specify range plotted on x-axis; usage: `choose_xrange=[xmin, xmax]`, xmin and xmax are of type: float, if not given uses data values to set axis limits\n",
+    "\n",
+    " - `choose_yrange = None`: specify range plotted on y-axis; usage: `choose_xrange=[ymin, ymax]`, ymin and ymax are of type: float, if not given uses data values to set axis limits\n",
     "\n",
     " - `silent = False`: switch off widgets and plot, important for use with multicontrollers\n",
     "\n",
+    "\n",
+    "- valid only for `multiagent()`:\n",
+    "\n",
+    " - `netType = 'full'`: type of network. Available types are: `full`, `erdos-renyi`, `barabasi-albert`, `dynamic` (see more information about their meaning above)\n",
+    " - `netParam`: this parameters has a specific meaning depending on the `netType`, see details above\n",
+    " - `motionCorrelatedness = 0.5`: (only for `netType`== `dynamic`) motion correlatedness of the agent. Correlatedness = 1 correponds to straight movement, Correlatedness = 0 corresponds to uncorrelated random walk.\n",
+    " - `particleSpeed = 0.01`: (only for `netType`== `dynamic`) speed of the agent, i.e. displacement in one timestep\n",
+    " - `showTrace = False`: (only for `netType`== `dynamic`) flag to show the motion trajectory of the agents\n",
+    " - `showInteractions = False`: (only for `netType`== `dynamic`) flag to show interactions; agents within communication range are liked through a line\n",
+    " - `timestepSize`: length of one timestep; the maximum timestep is determined by the rates\n",
+    "\n",
     "##### Keyword arguments for `integrate()` and `noiseCorrelations()`\n",
     "\n",
     "- valid for both methods:\n",
@@ -1856,7 +1882,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.4"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

mumot/controllers.py

@@ -1023,6 +1023,21 @@ def __init__(self, controllers, params=None, initWidgets=None, **kwargs):
                 inputValue = kwargs.get(key)
                 ep1 = None
                 ep2 = None
+                if key == 'xlab':
+                    for controller in controllers:
+                        controller._view._xlab = kwargs.get('xlab')
+                if key == 'ylab':
+                    for controller in controllers:
+                        controller._view._ylab = kwargs.get('ylab')
+                if key == 'fontsize':
+                    for controller in controllers:
+                        controller._view._axes_font_size = kwargs.get('fontsize')
+                if key == 'legend_loc':
+                    for controller in controllers:
+                        controller._view._legend_loc = kwargs.get('legend_loc')
+                if key == 'legend_fontsize':
+                    for controller in controllers:
+                        controller._view._legend_fontsize = kwargs.get('legend_fontsize')
                 if key == 'choose_yrange':
                     for controller in controllers:
                         controller._view._chooseYrange = kwargs.get('choose_yrange')

mumot/models.py

@@ -764,7 +764,7 @@ def integrate(self, showStateVars=None, initWidgets=None, **kwargs):
             variables (at time t=0) sum up to 1, or not. Defaults to False.
         legend_fontsize: int, optional
             Specify fontsize of legend.  Defaults to 14.
-        legend_loc : str
+        legend_loc : str, optional
             Specify legend location: combinations like 'upper left' (default),
             'lower right', or 'center center' are allowed (9 options in total).
         fontsize : integer, optional
@@ -1461,6 +1461,18 @@ def multiagent(self, initWidgets=None, **kwargs):
            (active only for netType='dynamic') flag to plot the trajectory of each reactant. Defaults to False.
         showInteractions : bool, optional
            (active only for netType='dynamic') flag to plot the interaction range between particles. Defaults to False.
+                legend_fontsize: int, optional
+            Specify fontsize of legend.  Defaults to 14.
+        legend_loc : str, optional
+            Specify legend location: combinations like 'upper left' (default), 'lower right', or 'center center' are allowed (9 options in total).
+        fontsize : integer, optional
+            Specify fontsize for axis-labels.  If not specified, the fontsize is automatically derived from the length of axis label.
+        xlab : str, optional
+            Specify label on x-axis.   Defaults to 'time t'.
+        ylab : str, optional
+            Specify label on y-axis.   Defaults to 'reactants'.
+        choose_xrange : list of float, optional
+            Specify range plotted on x-axis as a two-element iterable of the form [xmin, xmax]. If not given uses data values to set axis limits.
         silent : bool, optional
             Switch on/off widgets and plot. Important for use with multicontrollers. Defaults to False.
 
@@ -1625,6 +1637,16 @@ def SSA(self, initWidgets=None, **kwargs):
            Number of simulation runs to be executed. Must be strictly positive. Defaults to 1.
         aggregateResults : bool, optional
            Flag to aggregate or not the results from several runs. Defaults to True.
+        legend_loc : str, optional
+            Specify legend location: combinations like 'upper left' (default), 'lower right', or 'center center' are allowed (9 options in total).
+        fontsize : integer, optional
+            Specify fontsize for axis-labels.  If not specified, the fontsize is automatically derived from the length of axis label.
+        xlab : str, optional
+            Specify label on x-axis.   Defaults to 'time t'.
+        ylab : str, optional
+            Specify label on y-axis.   Defaults to 'reactants'.
+        choose_xrange : list of float, optional
+            Specify range plotted on x-axis as a two-element iterable of the form [xmin, xmax]. If not given uses data values to set axis limits.
         silent : bool, optional
             Switch on/off widgets and plot. Important for use with multicontrollers. Defaults to False.