1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
|
<html>
<head>
<title>Plotting Time Series Data</title>
</head>
<body>
<h1>Plotting Time Series Data</h1>
<p>
Open the file <tt>examples/cain/WilkinsonSMfSB/autoreg-2-1.xml</tt>.
Then select all of the species and reactions in the recorder panel.
(All of the species are selected by default. Switch to the Reactions
tab and then hit the <img src="add.png">
button to add all of the reactions.)
Next generate 10 trajectories using the defined model and method
by entering 10 in the Trajectories field and hitting the launch
button <img src="launch.png">.
Then click the plotting button <img src="plot.png">
in the simulation output panel. This will bring up the plot
configuration window shown below.
</p>
<p align="center">
<!--Resize to fit the window contents before capturing.-->
<img src="VisualizationPlottingWindowAutoregSpecies.jpg">
</p>
<p>
The plot configuration window consists of two tabs, one for time
series output and one for histogram output. Since we just generated
10 trajectories recorded with time series data we will work with the
former. At the top of the window is a drop-down box for choosing
the simulation output to plot. The output is described by the
model and method that was used to generate it.
</p>
<p>
Below the output selection are two rows
of radio buttons. In the first row one selects whether to plot species
populations, cumulative reaction counts, or binned reaction counts.
The binned reactions counts are the number of reaction events that
occur between the time frames. Note that only the species and
reactions that were selected in the recorder panel when the simulation
was run are available for plotting. By default all of the species are
selected and the reactions are not. In the second row of radio buttons,
one selects whether to plot trajectories, the mean (and optionally
the standard deviation shown as an error bar), or the standard
deviation.
</p>
<p>
Note that for simulation output that records all of the reaction
events the Binned Reactions radio button is disabled as there are
no fixed time frames. Also the statistics radio button is disabled;
one may only plot the trajectories.
</p>
<p>
Next is a grid which lists either the species or reactions in the
column headers. The row headers describe configuration options for the
lines which plot either the trajectories or statistics. One may edit
the grid cells individually or click on the column headers to modify
values for all rows. The columns have the following behavior:
<ul>
<li> <b>Show</b> - If the check box is selected, then the item will
be plotted. Clicking on a cell will toggle the state. Left/right clicking
on the column header will select/deselect all of the items.
<li> <b>Std Dev</b> - This column is only visible when plotting
statistics. If selected, a standard deviation bar will be shown at
each frame. Left/right clicking on the column header will
select/deselect all of the items.
<li> <b>Line Color</b> - Clicking on a cell will bring up a color
palette dialog. Left clicking on the column header with assign a
different color to each selected item using a range of hues. Right
clicking on the header will set all of the line colors to black.
<li> <b>Style</b> - The line style may be solid, dashed, dash-dot,
or dot. Clicking on cell will activate a drop-down box. Left
clicking on the column header will cycle between the styles for the
selected items. Right clicking will reset all of the line styles to
solid.
<li> <b>Width</b> - The line width is a positive integer. Clicking
on a cell will activate a spinner editor. Left/right clicking on the
column header will increment/decrement each of the widths.
<li> <b>Marker Style</b> - A variety of marker styles are available.
By default no marker is plotted. If a marker style is selected it
will appear at each frame. Click on a cell to activate a drop-down
box of styles. Left click on the column header to cycle between the
styles for the selected items. Right click to turn off markers for
all items.
<li> <b>Size</b> - The marker size is a positive integer, which may
be edited for each item. Left/right clicking on the
column header will increment/decrement each of the sizes.
<li> <b>Face Color</b> - The face color is the color of the interior
portion of the marker. Clicking on a cell will bring up a color
palette dialog. Left clicking on the column header will color the
selected items by hue. Right clicking will set all of the colors to
black.
<li> <b>Edge Color</b> - The edge color is the color of the boundary
of the marker. It may be edited in the same manner as the face color.
<li> <b>Edge Width</b> - The edge width is positive integer that may
be edited like the line width and marker size.
<li> <b>Legend Label</b> - Left clicking on the column header will
set these labels to the row labels, which are either the species
or reaction identifiers. Right clicking on the column header will
clear the labels. By clicking on a cell one may edit a single label.
</ul>
</p>
<p>
At the bottom of the plot configuration window one may select whether
the legend will be displayed. For this legend one may also choose the
font size and location. Next one may customize the size of the tick
labels on the axes. One may enter the title and
axes labels if desired. For these one may select the text color by
clicking the color button or change the text size by choosing from the
pull-down menu.
</p>
<p>
When data is plotted, a domain will be chosen that contains all of the
data points. You may change this behavior by explicitly setting the
lower and upper limits of the X and Y axes. Note that you may enter
any subset of these four limits. Any omitted limits will be
automatically calculated. Finally, one may specify the size of the
plotting window.
</p>
<p>
Below is a plotting window for the
auto-regulatory system. The legend has been placed in the upper left
corner. We have added a title and axes labels.
</p>
<p align="center">
<img src="VisualizationPlottingAutoregSpeciesFigure.jpg">
</p>
<p>
Note that there is a toolbar at the top of the plotting
window. Positioning the mouse pointer over these will bring up tool
tips which describe their functionality. The most important feature is
the last button, which is used to save the figure to a file.
Depending on the version of the matplotlib library installed, not all
file formats may be supported.
</p>
<!--CONTINUE: Verify that saving plots works on Windows.-->
<p>
See the <a href="Examples.htm">Examples</a> chapter for a variety of
sample plots.
</p>
</body>
</html>
|
