WIP: document deproj class methods.

DeProjMethods.md

@@ -32,7 +32,7 @@ o =
 
 ### Main `epicell` methods.
 
-There are no important user methods for `epicell`. All the important information is already in the properties. 
+There are no important user methods for `epicell`. All the important information is already in the properties. Check the [documentation on properties](DeProjProperties.md).
 
 ### Secondary `epicell` methods.
 
@@ -200,8 +200,132 @@ The first output arguments `f3d` contains the ellipse parameter in cartesian for
 
 The second argument `R` is the rotation matrix computed from the Euler angles.
 
+
+
 ## The `deproj` class methods.
 
+A `deproj` instance has several interesting methods, that let you export and display the analysis results. In particular the plotting routines: you will most likely be adapting them to your needs with a bit of MATLAB.
+
+In the following we suppose that `dpr` is an instance of `deproj`, for instance obtained by executing the a [self-contained example](RunExample.m) in this repository:
+
+```matlab
+>> dpr
+
+dpr = 
+
+  deproj with properties:
+
+          epicells: [426×1 epicell]
+    junction_graph: [1×1 graph]
+             units: 'µm'
+```
+
 ### Main `deproj` methods.
 
+#### `to_table`
+
+`T = to_table( obj )`
+
+Export masurements to a MATLAB table.
+
+```matlab
+>> T = dpr.to_table;
+>> head(T)
+
+ans =
+
+  8×23 table
+
+    id      xc        yc        zc        area     perimeter    euler_alpha     ...
+    __    ______    ______    _______    ______    _________    ___________     ...
+
+    1     1.3039    22.669    0.61254     2.507     7.2365        0.71603       ...
+    2     2.4739    23.827    0.66689    8.0899     11.849        0.90395       ...
+    3     3.5615    3.6656     5.0947    12.317     15.599        -2.0397       ...
+    4     2.4705    11.183     3.1008    8.0176     12.523        -2.0734       ...
+    5     2.6884    26.749    0.24663     5.141     9.1999        -2.1016       ...
+    6     3.6096    14.773     2.7521    13.812     16.114        -2.1033       ...
+    7     5.0077    8.8491     4.6461    40.057       26.8        -2.0163       ...
+    8     3.9601    29.361    0.22428    7.6378     11.323        -2.0704       ...
+```
+
+The table also stores the physical units of each columns:
+
+```matlab
+>> T.Properties.VariableUnits
+
+ans =
+
+  1×23 cell array
+
+  Columns 1 through 7
+
+    {0×0 char}    {'µm'}    {'µm'}    {'µm'}    {'µm²'}    {'µm'}    {'radians'} ...
+```
+
+A short description of the columns is present:
+
+```matlab
+>> T.Properties.VariableDescriptions{7}
+
+ans =
+
+    'First Euler angle for the cell plane (rotation around Z)'
+```
+
+And a table description:
+
+```matlab
+>> T.Properties.Description
+
+ans =
+
+    'Data generated from DeProj software, exported on 21-Jul-2020 23:07:02.'
+```
+
+#### `to_file`
+
+`to_file( obj, file_name, include_header )`
+
+Exports results to a spreadsheet file. 
+
+If `file_name` has `.csv` as extension, the data is saved as a CSV file. If it has `.xlsx` as an extension, it is saved as an Excel spreadsheet. The boolean flag `include_header` specifies whether the file will have a header with column names and units.
+
+```matlab
+dpr.to_file( 'table.csv' )
+dpr.to_file( 'table.xlsx' )
+```
+
+![ExampleExport](static/ExampleExport.png)
+
+#### `plot_sizes`
+
+`[ hf, ax1, ax2 ] = plot_sizes( obj, scale_bar_length )`
+
+Generate a figure with the cells area and perimeter. All the plots generated by the `plot_*` methods are 3D plots. The cells are drawn with their 3D coordinates and you can zoom, rotate, pan to make the curvature of the tissue appear. 
+
+The `scale_bar_length` parameter specifies what should be the length (in physical units) of the scale bar added to the bottom left of the plot. By default it is 10. The output arguments `[ hf, ax1, ax2 ]` are respectfully the handles to the figure created, to the top axes and to the bottom axes. 
+
+```matlab
+>> dpr.plot_sizes
+```
+
+![ExampleResults_fig1a_CellSize](static/ExampleResults_fig1a_CellSize.png)
+
+#### `plot_fit_plane`
+
+`[ hf, ax1, ax2, ax3 ] = plot_fit_plane( obj, scale_bar_length )`
+
+Generate a figure with the local plane orientation for each cell. This orientation is given as 3 Euler angles in the [ZX'Z'' convention](https://en.wikipedia.org/wiki/Euler_angles#Chained_rotations_equivalence). 
+
+- The first one, `alpha` is the orientation of the cell plane (top panel below). As an analogy, imaging you are facing a hill, the slope going up. The direction (south, west…) in which the slope is the largest is given by the angle `alpha`. On these figures we wrap the angle between 0º and 180º to and because of MATLAB convention, this angle is measured counterclockwise from the Y axis (so 90º corresponds to a slope going up in the east-west direction).
+- The second one, `beta` measures the slope of this plane with XY plane (middle panel). A value of 0º indicates that the cell plane is parallel to XY. 
+- The third one , `gamma` measures the cell main orientation in the cell plane (bottom panel). Because the cell plane was rotated a first time by `alpha`, this angle does not give a result immediately usable. 
+
+```matlab
+>> dpr.plot_fit_plane
+```
+
+![ExampleResults_fig2_EulerAngles](static/ExampleResults_fig2_EulerAngles.png)
+
 ### Secondary `deproj` methods.
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