The first three axes (Voltage axis, Current axis and State axis) are used to plot variables vs. time. Each of these require their own graph because the method used to solve the cable equations evaluates these variables at different times. For example, voltages are calculated at each time step, but currents are calculated at the half time step before voltage and the state variables are calculated at the half time step after the voltage. For more information on the numerical method used to solve these equations see Hines, 1984.
Graph types 1 - 5 are coupled to the standard run procedure so that the value of the function is plotted. (See "Run Control Panel"). "Clicking" on one of the first three choices immediately brings up a graphic window with time as the absissa. The steps in achieving the desired simulation plot are as follows:
1. Selecting a "Voltage" axis from the "New Graph" menu in the NEURON Main Panel opens a new graph window with axes
( Y axis: -80 mV to +40 mV; X axis: 0 to Tstop )
2. Selecting " Current axis" from the "New Graph" menu in the NEURON Main Panel opens a new graph window with axes
(Y axis: -1 to +1nA; X axis: 0 to Tstop ).
3. Selecting " State axis" from the "New Graph" menu in the NEURON Main Panel opens a new graph window for plotting state variables:
(Y axis: 0 to +1; X axis: 0 to Tstop ).
5. Selecting "Phase plane" opens a graphic window for plotting
f(t) vs g(t)
6. Selecting "Grapher" opens a gemeral purpose panel
suited for a variety of uses. For example. it can be used as a batch program in which
a parameter is changed incrementally to yield a family of solutions. A trival example
is the plotting of an algebraic expression as shown here. In this case, no "generator"
was entered. the default axes and
independent variable "t" were
accepted, and the sine and cosine functions entered in the edit box of the "Plot What" browser.
Another example of the use of grapher is to graph the
steady-state values of the m, h, n state variables in the HH equations. These
steady-states are calculated for v_init, the initial value of the membrane potential,
whenever the procedure init() is called. Thus v_init was entered for the independent variable,
init() was entered for the generator; the "set View" graphic window option was used
to set the voltage axis to the desired range and the y axis from 0 to 1. The state
variables (in the soma) were entered in the "Plot What" browser and the colors changed.
Pressing "Plot" then produced the plots shown below.
The "grapher" is also very useful in producing a summary plot of a run of simulations. For example, it is interesting to the peak of the action potential in the soma as a function of the synaptic input condctance on a particular dendrite (as for example in the "Shape Plot" of our simple nerve cell with three dendrites shown above). This is a more complex problem but was solved rather easily by:
proc advance() {local vsoma
fadvance() vsoma=soma.v(.5)
if (t<=dt || vsoma > vmax) {vmax=vsoma}
// whenever the "if" condition is met the expression
// within the right braces is carried out
}
In another window, the membrane voltage in the axon and soma were plotted as in this figure below which was taken under slightly different conditions of range and number of steps. From this figure it is clear that
A variety of views of graphs are also available from the "Plot menu" (right mouse button in the plotting field). These are described in detail in Scene & View Options .