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--------------
Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI
===============================================================
Upinder Bhalla, Harsha Rani
Feb 25 2016.
--------------
- `Introduction <#introduction>`_
- `**TODO** What are chemical kinetic
models? <#todo-what-are-chemical-kinetic-models>`_
- `Levels of model <#levels-of-model>`_
- `Numerical methods <#numerical-methods>`_
- `Using Kinetikit 12 <#using-kinetikit-12>`_
- `Overview <#overview>`_
- `Model layout and icons <#model-layout-and-icons>`_
- `Compartment <#compartment>`_
- `Pool <#pool>`_
- `Buffered pools <#buffered-pools>`_
- `Reaction <#reaction>`_
- `Mass-action enzymes <#mass-action-enzymes>`_
- `Michaelis-Menten Enzymes <#michaelis-menten-enzymes>`_
- `Function <#function>`_
- `Model operations <#model-operations>`_
- `Model Building <#model-building>`_
`Introduction <#TOC>`_
----------------------
Kinetikit 12 is a graphical interface for doing chemical kinetic
modeling in MOOSE. It is derived in part from Kinetikit, which was the
graphical interface used in GENESIS for similar models. Kinetikit, also
known as kkit, was at version 11 with GENESIS. Here we start with
Kinetikit 12.
`**TODO** What are chemical kinetic models? <#TOC>`_
----------------------------------------------------
Much of neuronal computation occurs through chemical signaling. For
example, many forms of synaptic plasticity begin with calcium influx
into the synapse, followed by calcium binding to calmodulin, and then
calmodulin activation of numerous enzymes. These events can be
represented in chemical terms:
4 Ca2+ + CaM <===> Ca4.CaM
Such chemical equations can be modeled through standard Ordinary
Differential Equations, if we ignore space:
d[Ca]/dt = −4Kf ∗ [Ca]4 ∗ [CaM] + 4Kb ∗ [Ca4.CaM] d[CaM]/dt = −Kf ∗
[Ca]4 ∗ [CaM] + Kb ∗ [Ca4.CaM] d[Ca4.CaM]/dt = Kf ∗ [Ca]4 ∗ [CaM] −
Kb ∗ [Ca4.CaM]
MOOSE models these chemical systems. This help document describes how to
do such modelling using the graphical interface, Kinetikit 12.
`Levels of model <#TOC>`_
~~~~~~~~~~~~~~~~~~~~~~~~~
Chemical kinetic models can be simple well-stirred (or point) models, or
they could have multiple interacting compartments, or they could include
space explicitly using reaction-diffusion. In addition such models could
be solved either deterministically, or using a stochastic formulation.
At present Kinetikit handles compartmental models but does not compute
diffusion within the compartments, though MOOSE itself can do this at
the script level. Kkit12 will do deterministic as well as stochastic
chemical calculations.
`Numerical methods <#TOC>`_
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- **Deterministic**: Adaptive timestep 5th order Runge-Kutta-Fehlberg
from the GSL (GNU Scientific Library).
- **Stochastic**: Optimized Gillespie Stochastic Systems Algorithm,
custom implementation.
`Using Kinetikit 12 <#TOC>`_
----------------------------
`Overview <#TOC>`_
~~~~~~~~~~~~~~~~~~
- Load models using **``File -> Load model``**. A reaction schematic
for the chemical system appears in the **``Editor view``** tab.
- View parameters in **``Editor view``** tab by clicking on icons, and
looking at entries in **``Properties``** table to the right.
- Edit parameters by changing their values in the **``Properties``**
table.
- From Run View, Pools can be plotted by clicking on their icons and
dragging the icons onto the plot Window. Presently only concentration
is plottable.
- Run models using **``Run``** button.
- Select numerical method using options under **``Preferences``**
button in simulation control.
- Save plots using the icons at the bottom of the **``Plot Window``**.
Most of these operations are detailed in other sections, and are shared
with other aspects of the MOOSE simulation interface. Here we focus on
the Kinetikit-specific items.
`Model layout and icons <#TOC>`_
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When you are in the **``Model View``** (``Editor``) tab you will see a collection of
icons, arrows, and grey boxes surrounding these. This is a schematic of
the reaction scheme being modeled. You can view and change parameters,
and change the layout of the model.
.. figure:: ../../images/Moose1.png
:align: center
:alt:
Resizing the model layout and icons:
- **Zoom**: Comma and period keys. Alternatively, the mouse scroll
wheel or vertical scroll line on the track pad will cause the display
to zoom in and out.
- **Pan**: The arrow keys move the display left, right, up, and down.
- **Entire Model View**: Pressing the **``a``** key will fit the entire
model into the entire field of view.
- **Resize Icons**: Angle bracket keys, that is, **``<``** and
**``>``** or **``+``** and **``-``**. This resizes the icons while
leaving their positions on the screen layout more or less the same.
- **Original Model View**: Presing the **``A``** key (capital ``A``)
will revert to the original model view including the original icon
scaling.
`Compartment <#TOC>`_
^^^^^^^^^^^^^^^^^^^^^
The *compartment* in moose is usually a contiguous domain in which a
certain set of chemical reactions and molecular species occur. The
definition is very closely related to that of a cell-biological
compartment. Examples include the extracellular space, the cell
membrane, the cytosol, and the nucleus. Compartments can be nested, but
of course you cannot put a bigger compartment into a smaller one.
- **Icon**: Grey boundary around a set of reactions.
- **Moving Compartments**: Click and drag on the boundary.
- **Resizing Compartment boundary**: Happens automatically when
contents are repositioned, so that the boundary just contains
contents.
- **Compartment editable parameters**:
- **``name``**: The name of the compartment.
- **``size``**: This is the volume, surface area or length of the
compartment, depending on its type.
- **Compartment fixed parameters**:
- **``numDimensions``**: This specifies whether the compartment is a
volume, a 2-D surface, or if it is just being represented as a
length.
`Pool <#TOC>`_
^^^^^^^^^^^^^^
This is the set of molecules of a given species within a compartment.
Different chemical states of the same molecule are in different pools.
- **Icon**: |image0| Colored rectangle with pool name in it.
- **Moving pools**: Click and drag.
- **Pool editable parameters**:
- **``name``**: Name of the pool
- **``n``**: Number of molecules in the pool
- **``nInit``**: Initial number of molecules in the pool. ``n`` gets
set to this value when the ``reinit`` operation is done.
- **``conc``**: Concentration of the molecules in the pool.
conc = n \* unit\_scale\_factor / (NA \* vol)
- **``concInit``**: Initial concentration of the molecules in the
pool.
concInit = nInit \* unit\_scale\_factor / (NA \* vol) ``conc``
is set to this value when the ``reinit`` operation is done.
- **Pool fixed parameters**
- **``size``**: Derived from the compartment that holds the pool.
Specifies volume, surface area or length of the holding
compartment.
`Buffered pools <#TOC>`_
^^^^^^^^^^^^^^^^^^^^^^^^
Some pools are set to a fixed ``n``, that is number of molecules, and
therefore a fixed concentration, throughout a simulation. These are
buffered pools.
- **Icon**: |image1| Colored rectangle with pool name in it.
- **Moving Buffered pools**: Click and drag.
- **Buffered Pool editable parameters**
- **``name``**: Name of the pool
- **``nInit``**: Fixed number of molecules in the pool. ``n`` gets
set to this value throughout the run.
- **``concInit``**: Fixed concentration of the molecules in the
pool.
concInit = nInit \* unit\_scale\_factor / (NA \* vol) ``conc``
is set to this value throughout the run.
- **Pool fixed parameters**:
- **``n``**: Number of molecules in the pool. Derived from
``nInit``.
- **``conc``**: Concentration of molecules in the pool. Derived from
``concInit``.
- **``size``**: Derived from the compartment that holds the pool.
Specifies volume, surface area or length of the holding
compartment.
`Reaction <#TOC>`_
^^^^^^^^^^^^^^^^^^
These are conversion reactions between sets of pools. They are
reversible, but you can set either of the rates to zero to get
irreversibility. In the illustration below, **``D``** and **``A``** are
substrates, and **``B``** is the product of the reaction. This is
indicated by the direction of the green arrow.
.. figure:: ../../images/KkitReaction.png
:align: center
:alt:
- **Icon**: |image2| Reversible reaction arrow.
- **Moving Reactions**: Click and drag.
- **Reaction editable parameters**:
- name : Name of reaction
- K\ :sub:`f`\ : Forward rate of reaction, in
``concentration/time`` units. This is the normal way to express
and manipulate the reaction rate.
- k\ :sub:`f`\ : Forward rate of reaction, in ``number/time``
units. This is used internally for computations, but is
volume-dependent and should not be used to manipulate the reaction
rate unless you really know what you are doing.
- K\ :sub:`b`\ : Backward rate of reaction, in
``concentration/time`` units. This is the normal way to express
and manipulate the reaction rate.
- k\ :sub:`b`\ : Backward rate of reaction, in ``number/time``
units. This is used internally for computations, but is
volume-dependent and should not be used to manipulate the reaction
rate unless you really know what you are doing.
- **Reaction fixed parameters**:
- **numProducts**: Number of product molecules.
- **numSubstrates**: Number of substrates molecules.
`Mass-action enzymes <#TOC>`_
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are enzymes that model the chemical equations
E + S <===> E.S -> E + P
Note that the second reaction is irreversible. Note also that
mass-action enzymes include a pool to represent the **``E.S``**
(enzyme-substrate) complex. In the example below, the enzyme pool is
named **``MassActionEnz``**, the substrate is **``C``**, and the product
is **``E``**. The direction of the enzyme reaction is indicated by the
red arrows.
.. figure:: ../../images/MassActionEnzReac.png
:align: center
:alt:
- **Icon**: |image3| Colored ellipse atop a small square. The ellipse
represents the enzyme. The small square represents **``E.S``**, the
enzyme-substrate complex. The ellipse icon has the same color as the
enzyme pool **``E``**. It is connected to the enzyme pool **``E``**
with a straight line of the same color.
The ellipse icon sits on a continuous, typically curved arrow in red,
from the substrate to the product.
A given enzyme pool can have any number of enzyme activities, since
the same enzyme might catalyze many reactions.
- **Moving Enzymes**: Click and drag on the ellipse.
- **Enzyme editable parameters**
- name : Name of enzyme.
- K\ :sub:`m`\ : Michaelis-Menten value for enzyme, in
``concentration`` units.
- k\ :sub:`cat`\ : Production rate of enzyme, in ``1/time`` units.
Equal to k\ :sub:`3`\ , the rate of the second, irreversible
reaction.
- k\ :sub:`1`\ : Forward rate of the **E+S** reaction, in number
and ``1/time`` units. This is what is used in the internal
calculations.
- k\ :sub:`2`\ : Backward rate of the **E+S** reaction, in
``1/time`` units. Used in internal calculations.
- k\ :sub:`3`\ : Forward rate of the **E.S -> E + P** reaction, in
``1/time`` units. Equivalent to k\ :sub:`cat`\ . Used in internal
calculations.
- ratio: This is equal to k\ :sub:`2`\ /k\ :sub:`3`\ . Needed to
define the internal rates in terms of K\ :sub:`m`\ and
k\ :sub:`cat`\ . I usually use a value of 4.
- **Enzyme-substrate-complex editable parameters**: These are identical
to those of any other pool.
- **name**: Name of the **``E.S``** complex. Defaults to
**``<enzymeName>_cplx``**.
- **n**: Number of molecules in the pool
- **nInit**: Initial number of molecules in the complex. ``n`` gets
set to this value when the ``reinit`` operation is done.
- **conc**: Concentration of the molecules in the pool.
conc = n \* unit\_scale\_factor / (NA \* vol)
- **``concInit``**: Initial concentration of the molecules in the
pool.
concInit = nInit \* unit\_scale\_factor / (NA \* vol) ``conc``
is set to this value when the ``reinit`` operation is done.
- **Enzyme-substrate-complex fixed parameters**:
- **size**: Derived from the compartment that holds the pool.
Specifies volume, surface area or length of the holding
compartment. Note that the Enzyme-substrate-complex is assumed to
be in the same compartment as the enzyme molecule.
`Michaelis-Menten Enzymes <#TOC>`_
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are enzymes that obey the Michaelis-Menten equation
V = Vmax \* [S] / ( Km + [S] ) = kcat \* [Etot] \* [S] / ( Km + [S]
)
where
- V\ :sub:`max`\ is the maximum rate of the enzyme
- [Etot] is the total amount of the enzyme
- K\ :sub:`m`\ is the Michaelis-Menten constant
- S is the substrate.
Nominally these enzymes model the same chemical equation as the
mass-action enzyme:
E + S <===> E.S -> E + P
but they make the assumption that the **``E.S``** is in a
quasi-steady-state with **``E``** and **``S``**, and they also ignore
sequestration of the enzyme into the complex. So there is no
representation of the **``E.S``** complex. In the example below, the
enzyme pool is named **``MM_Enz``**, the substrate is **``E``**, and the
product is **``F``**. The direction of the enzyme reaction is indicated
by the red arrows.
.. figure:: ../../images/MM_EnzReac.png
:align: center
:alt:
- **Icon**: |image4| Colored ellipse. The ellipse represents the enzyme
The ellipse icon has the same color as the enzyme **``MM_Enz``**. It
is connected to the enzyme pool **``MM_Enz``** with a straight line
of the same color. The ellipse icon sits on a continuous, typically
curved arrow in red, from the substrate to the product. A given
enzyme pool can have any number of enzyme activities, since the same
enzyme might catalyze many reactions.
- **Moving Enzymes**: Click and drag.
- **Enzyme editable parameters**:
- name: Name of enzyme.
- K\ :sub:`m`\ : Michaelis-Menten value for enzyme, in
``concentration`` units.
- k\ :sub:`cat`\ : Production rate of enzyme, in ``1/time`` units.
Equal to k\ :sub:`3`\ , the rate of the second, irreversible
reaction.
`Function <#TOC>`_
^^^^^^^^^^^^^^^^^^
Function objects can be used to evaluate expressions with arbitrary
number of variables and constants. We can assign expression of the form:
f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )
where ci‘s are constants and xi‘s and yi‘s are variables.
It can parse mathematical expression defining a function and evaluate it
and/or its derivative for specified variable values. The variables can
be input from other moose objects. In case of arbitrary variable names,
the source message must have the variable name as the first argument.
- **Icon**: Colored rectangle with pool name. This is **``ƒ``** in the
example image below. The input pools **``A``** and **``B``** connect
to the **ƒ** with blue arrows. The function ouput's to BuffPool
`Model operations <#TOC>`_
~~~~~~~~~~~~~~~~~~~~~~~~~~
- **Loading models**: **``File -> Load Model -> select from dialog``**.
This operation makes the previously loaded model disable and loads
newly selected models in **``Model View``**
- **New**: **``File -> New -> Model name``**. This opens a empty widget
for model building
- **Saving models**: **``File -> Save Model -> select from dialog``**.
- **Changing numerical methods**: **``Preference->Chemical tab``** item
from Simulation Control. Currently supports:
- Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from
the GNU Scientific Library (GSL). It is a fifth order variable
timestep explicit method. Works well for most reaction systems
except if they have very stiff reactions.
- Gillespie: Optimized Gillespie stochastic systems algorithm,
custom implementation. This uses variable timesteps internally.
Note that it slows down with increasing numbers of molecules in
each pool. It also slows down, but not so badly, if the number of
reactions goes up.
- Exponential Euler:This methods computes the solution of partial
and ordinary differential equations.
`Model building <#TOC>`_
~~~~~~~~~~~~~~~~~~~~~~~~
.. figure:: ../../images/chemical_CS.png
:align: center
:alt:
- The Edit Widget includes various menu options and model icons on the
top.\* Use the mouse buttton to click and drag icons from toolbar to
Edit Widget, two things will happen, icon will appear in the editor
widget and a object editor will pop up with lots of parameters with
respect to moose object. Rules:
::
* Firstly Compartment has to be created.
(At present only single compartment model is allowed)
- Enzyme should be dropped on a pool as parent and function should
be dropped on buffPool for output
- Drag in pool's and reaction on to the editor widget, now one can
set up a reaction.Click on mooseObject drag the mouse (a black dotted line for ExpectedConnection will appear)
to any object for connection.
E.g Pool to reaction and reaction to pool. Pool to function and function to Pool.
Specific connection type gets specific colored arrow. E.g.
Green color arrow for specifying connection between reactant and
product for reaction. Second order reaction can also be done by
repeating the connection over again
- Each connection can be deleted and using rubberband selection each moose object can be deleted
- When clicked on pool object 4 icons comes up
|delete| : This deletes the object, its associated connection and if its enzyme's parent then enzyme and its associated connection is also deleted.
|clone| : Clones the object
|move| : Object can be moved around
|plot| : Plot the object in plotWidget at Graph 1
Note: Missing icon means the operation is not permitted
.. figure:: ../../images/Chemical_run.png
:align: center
:alt:
- From run widget, pools are draggable to plot window for plotting.
(Currently **``conc``** is plotted as default field) Plots are
color-coded as per in model.
- Model can be run by clicking start button. One can stop button in
mid-stream and start up again without affectiong the calculations.
The reset button clears the simulation.
.. |image0| image:: ../../images/Pool.png
.. |image1| image:: ../../images/BufPool.png
.. |image2| image:: ../../images/KkitReacIcon.png
.. |image3| image:: ../../images/MassActionEnzIcon.png
.. |image4| image:: ../../images/MM_EnzIcon.png
.. |delete| image:: ../../images/delete.png
.. |clone| image:: ../../images/clone.png
.. |move| image:: ../../images/move.png
.. |plot| image:: ../../images/plot.png
\ No newline at end of file
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--------------
**MOOSE GUI: Graphical interface for MOOSE**
============================================
Upinder Bhalla, Harsha Rani, Aviral Goel
Aug 28 2013.
--------------
Contents
--------
- `Introduction <#introduction>`_
- `Interface <#interface>`_
- `Menu Bar <#menu-bar>`_
- `File <#menu-file>`_
- `New <#file-new>`_
- `Load Model <#file-load-model>`_
- `Connect BioModels <#file-connect-biomodels>`_
- `Quit <#file-quit>`_
- `View <#menu-view>`_
- `Editor View <#editor-view>`_
- `Run View <#run-view>`_
- `Dock Widgets <#dock-widgets>`_
- `SubWindows <#subwindows>`_
- `Help <#menu-help>`_
- `About MOOSE <#about-moose>`_
- `Built-in Documentation <#built-in-documentation>`_
- `Report a bug <#report-a-bug>`_
- `Editor View <#editor-view>`_
- `Model Editor <#model-editor>`_
- `Property Editor <#property-editor>`_
- `Run View <#run-view>`_
- `Simulation Controls <#simulation-controls>`_
- `Plot Widget <#plot-widget>`_
- `Toolbar <#plot-widget-toolbar>`_
- `Context Menu <#plot-widget-context-menu>`_
Introduction
------------
The Moose GUI currently allow you work on
`chemical <Kkit12Documentation.html>`_ models using a interface. This
document describes the salient features of the GUI
Interface
---------
The interface layout consists of a `menu bar <#menu-bar>`_ and two
views, `editor view <#editor-view>`_ and `run view <#run-view>`_.
Menu Bar
~~~~~~~~
.. figure:: ../../images/MooseGuiMenuImage.png
:align: center
:alt:
The menu bar appears at the top of the main window. In Ubuntu 12.04, the
menu bar appears only when the mouse is in the top menu strip of the
screen. It consists of the following options -
File
^^^^
The File menu option provides the following sub options -
- `New <#file-new>`_ - Create a new chemical signalling model.
- `Load Model <#file-load-model>`_ - Load a chemical signalling or
compartmental neuronal model from a file.
- `Paper\_2015\_Demos Model <#paper-2015-demos-model>`_ - Loads and
Runs chemical signalling or compartmental neuronal model from a file.
- `Recently Loaded Models <#recently-loaded-models>`_ - List of models
loaded in MOOSE. (Atleast one model should be loaded)
- `Connect BioModels <#file-connect-biomodels>`_ - Load chemical
signaling models from the BioModels database.
- `Save <#file-quit>`_ - Saves chemical model to Genesis/SBML format.
- `Quit <#file-quit>`_ - Quit the interface.
View
^^^^
View menu option provides the following sub options -
- `Editor View <#editor-view>`_ - Switch to the editor view for editing
models.
- `Run View <#run-view>`_ - Switch to run view for running models.
- `Dock Widgets <#dock-widgets>`_ - Following dock widgets are provided
-
- `Python <#dock-widget-python>`_ - Brings up a full fledged python
interpreter integrated with MOOSE GUI. You can interact with
loaded models and load new models through the PyMoose API. The
entire power of python language is accessible, as well as
MOOSE-specific functions and classes.
- `Edit <#dock-widget-edit>`_ - A property editor for viewing and
editing the fields of a selected object such as a pool, enzyme,
function or compartment. Editable field values can be changed by
clicking on them and overwriting the new values. Please be sure to
press enter once the editing is complete, in order to save your
changes.
- `SubWindows <#subwindows>`_ - This allows you to tile or tabify the
run and editor views.
Help
^^^^
- `About Moose <#about-moose>`_ - Version and general information about
MOOSE.
- `Built-in documentation <#butilt-in-documentation>`_ - Documentation
of MOOSE GUI.
- `Report a bug <#report-a-bug>`_ - Directs to the github bug tracker
for reporting bugs.
Editor View
~~~~~~~~~~~
The editor view provides two windows -
- `Model Editor <#model-editor>`_ - The model editor is a workspace to
edit and create models. Using click-and-drag from the icons in the
menu bar, you can create model entities such as chemical pools,
reactions, and so on. A click on any object brings its property
editor on screen (see below). In objects that can be interconnected,
a click also brings up a special arrow icon that is used to connect
objects together with messages. You can move objects around within
the edit window using click-and-drag. Finally, you can delete objects
by selecting one or more, and then choosing the delete option from
the pop-up menu. The links below is the screenshots point to the
details for the chemical signalling model editor.
.. figure:: ../../images/ChemicalSignallingEditor.png
:align: center
:alt: Chemical Signalling Model Editor
Chemical Signalling Model Editor
- `Property Editor <#property-editor>`_ - The property editor provides
a way of viewing and editing the properties of objects selected in
the model editor.
.. figure:: ../../images/PropertyEditor.png
:align: center
:alt: Property Editor
Property Editor
Run View
~~~~~~~~
The Run view, as the name suggests, puts the GUI into a mode where the
model can be simulated. As a first step in this, you can click-and-drag
an object to the graph window in order to create a time-series plot for
that object. For example, in a chemical reaction, you could drag a pool
into the graph window and subsequent simulations will display a graph of
the concentration of the pool as a function of time. Within the Run View
window, the time-evolution of the simulation is displayed as an
animation. For chemical kinetic models, the size of the icons for
reactant pools scale to indicate concentration. Above the Run View
window, there is a special tool bar with a set of simulation controls to
run the simulation.
Simulation Controls
^^^^^^^^^^^^^^^^^^^
.. figure:: ../../images/SimulationControl.png
:align: center
:alt: Simulation Control
Simulation Control
This panel allows you to control the various aspects of the simulation.
- `Run Time <#run-time>`_ - Determines duration for which simulation is
to run. A simulation which has already run, runs further for the
specified additional period.
- `Reset <#reset>`_ - Restores simulation to its initial state;
re-initializes all variables to t = 0.
- `Stop <#stop>`_ - This button halts an ongoing simulation.
- `Current time <#current-time>`_ - This reports the current simulation
time.
- `Preferences <#preferences>`_ - Allows you to set simulation and
visualization related preferences.
Plot Widget
^^^^^^^^^^^
Toolbar
'''''''
On top of plot window there is a little row of icons:
.. figure:: ../../images/PlotWindowIcons.png
:align: center
:alt:
These are the plot controls. If you hover the mouse over them for a few
seconds, a tooltip pops up. The icons represent the following functions:
- |image0| - Add a new plot window
- |image1| - Deletes current plot window
- |image2| - Toggle X-Y axis grid
- |image3| - Returns the plot display to its default position
- |image4| - Undoes or re-does manipulations you have done to the
display.
- |image5| - The plots will pan around with the mouse when you hold the
left button down. The plots will zoom with the mouse when you hold
the right button down.
- |image6| - With the **``left mouse button``**, this will zoom in to
the specified rectangle so that the plots become bigger. With the
**``right mouse button``**, the entire plot display will be shrunk to
fit into the specified rectangle.
- |image7| - You don't want to mess with these .
- |image8| - Save the plot.
Context Menu
''''''''''''
The context menu is enabled by right clicking on the plot window. It has
the following options -
- **Export to CSV** - Exports the plotted data to CSV format
- **Toggle Legend** - Toggles the plot legend
- **Remove** - Provides a list of plotted entities. The selected entity
will not be plotted.
.. |image0| image:: ../../images/Addgraph.png
.. |image1| image:: ../../images/delgraph.png
.. |image2| image:: ../../images/grid.png
.. |image3| image:: ../../images/MatPlotLibHomeIcon.png
.. |image4| image:: ../../images/MatPlotLibDoUndo.png
.. |image5| image:: ../../images/MatPlotLibPan.png
.. |image6| image:: ../../images/MatPlotLibZoom.png
.. |image7| image:: ../../images/MatPlotLibConfigureSubplots.png
.. |image8| image:: ../../images/MatPlotLibSave.png
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