how-to-use.md

 MapGenerator provides a huge set of options to plot maps from netCDF file(s) or from multi-dimensional arrays already retrieved and loaded in memory. It can be used basically in two ways:
 
-1.  by command line (needs netCDF to read):
+1.  by **command line** (needs netCDF to read):
 
 ```
 mg --help
@@ -10,7 +10,7 @@ mg --option1 value1 ... --optionN valueN
 mg --option1=value1 ... --optionN=valueN
 ```
 
-2.  as python library:
+2.  as **python library**:
 
 ```
 from mapgenerator.plotting import plotmap
@@ -22,7 +22,7 @@ pm.plot(option1=value1, ..., optionN=valueN)  (reads from netCDF)
 pm.aplot(option1=value1, ..., optionN=valueN) (reads from array)
 ```
 
-Additionally, it can be used as an R library:
+Additionally, it can be used as an **R library**:
 
 ```
 library(reticulate)
@@ -35,4 +35,16 @@ pm$aplot(option1=value1, ..., optionN=valueN)
 
 ```
 
-All available options can be found [here](options)
+Options can be **passed directly** to the command line or to the functions plot and aplot or can be **stored in configuration files** stored according  to the following standard:
+
+```
+# comment
+[section]
+option1 = value1
+...
+optionN = valueN
+```
+
+If options are passed both directly and through configuration file, direct ones have priorities. This can be very useful if you have  a set of plots to draw with some options in common and others that change, the constant ones can be stored into one or more configuration files and the others passed directly.
+
+All available options can be found [here](options).