Merge pull request #9 from OCNS/feat/gnuplot

feat: add gnuplot snippet

source/00_gnuplot.md

@@ -0,0 +1,76 @@
+(cli:gnuplot)=
+# Plotting with GNUPlot
+
+When dealing with data either from simulations or from experiments, it's often useful to get quick previews without having to write complete Python scripts using numpy/matplotlib.
+[GNUPlot](http://www.gnuplot.info/) is a command line plotting tool that makes this very easy.
+One can also write complete plotting scripts in GNUPlot, but it can also be used directly from the command line without them.
+
+Requirements/setup:
+
+- Install GNUPlot. On most Linux distributions, it is available from the default package manager. Others can download it [from the website](http://www.gnuplot.info/download.html).
+- Have some data files you want to quickly plot/preview. An example data file is provided for you [here](./data/00_gnuplot.dat).
+- Access to a terminal (available on all Mac/Linux distributions, for Windows, something like Power shell will do)
+
+
+Let's take a quick look at the contents of the file
+
+```console
+$ head 00_gnuplot.dat
+0.0     -0.065  -0.065  -0.065  -0.065  -0.065
+5.0E-5  -0.065  -0.065  -0.065  -0.065  -0.065
+1.0E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+1.5E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+2.0E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+2.5E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+3.0E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+3.5E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+4.0E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+4.5E-4  -0.065  -0.065  -0.065  -0.065  -0.065
+```
+
+The first column is time, the rest are membrane potentials for different cells.
+Let us plot the membrane potential for a few cells:
+
+```console
+$ gnuplot -p -e "set xlabel 'time (s)'; set ylabel 'v (volt)' ;\
+    plot '00_gnuplot.dat' using 1:2 with lines title 'cell1'"
+```
+This will pop up a window like this:
+
+```{figure} images/00_gnuplot_1.png
+:alt: screnshot showing a GNUPlot window
+:align: center
+:width: 50%
+```
+
+You can use the controls to zoom in, out, or to save the figure to a file.
+Explanation of options and commands:
+
+- `-p` makes the GNUPlot window persist until closed by the user
+- `-e` executes the provided commands
+- the `using` key word is used to select columns to plot
+- `with lines` tells GNUPlot to plot using lines
+- `title` sets the title for this plot
+
+
+To plot multiple columns, one can use this:
+```console
+$ gnuplot -p -e "set xlabel 'time (s)'; set ylabel 'v (volt)' ;\
+    plot '00_gnuplot.dat' using 1:2 with lines title 'cell1',\
+    '' using 1:3 with lines title 'cell2'"
+```
+```{figure} images/00_gnuplot_2.png
+:alt: screnshot showing a GNUPlot window with two lines plotted
+:align: center
+:width: 50%
+```
+
+Here, the empty quotes implies that the same file should be used.
+
+GNUPlot has lots of advanced options such as exporting to LaTeX, statistics, for loops, multi-plots, and so on.
+Please check the references for more information.
+
+References
+
+- http://www.gnuplot.info/
+- https://learn.microsoft.com/en-us/powershell/

source/_toc.yml

@@ -1,4 +1,9 @@
 format: jb-book
 root: index
-chapters:
-  - file: Contributing.md
+parts:
+  - caption: Contributing
+    chapters:
+      - file: Contributing.md
+  - caption: Command line
+    chapters:
+      - file: 00_gnuplot.md