New doc for drawing functions

doc/api.md

@@ -4,6 +4,25 @@
 
 ---
 
+<a id="method__draw_matrix.1" class="lexicon_definition"></a>
+#### draw_matrix(M::Modular) [¶](#method__draw_matrix.1)
+
+Takes a `Modular` object, and plot it using the *Cairo* driver.
+
+**Keyword arguments:**
+
+- `reorder::Function`, a function to change the order of species (by default, `reorder_by_module!`)
+- `file`: the name of the file to draw in (has to end in `.png`)
+
+Note that the modules are identified by color, using the
+`distinguishable_colors` function from the `Colors` package.
+
+
+*source:*
+[Brim/src/draw_matrix.jl:44](file:///home/tpoisot/.julia/v0.3/Brim/src/draw_matrix.jl)
+
+---
+
 <a id="method__no_empty_modules.1" class="lexicon_definition"></a>
 #### no_empty_modules!(M::Modular) [¶](#method__no_empty_modules.1)
 
@@ -54,6 +73,18 @@ cannot have empty rows or columns.
 *source:*
 [Brim/src/permutations.jl:100](file:///home/tpoisot/.julia/v0.3/Brim/src/permutations.jl)
 
+---
+
+<a id="method__reorder_by_module.1" class="lexicon_definition"></a>
+#### reorder_by_module!(M::Modular) [¶](#method__reorder_by_module.1)
+
+Takes a `Modular` object, and reorder it by module. The row / columns of `A` and
+`S` are modified.
+
+
+*source:*
+[Brim/src/draw_matrix.jl:5](file:///home/tpoisot/.julia/v0.3/Brim/src/draw_matrix.jl)
+
 ## Internal
 
 ---
@@ -112,3 +143,4 @@ Also, this is a serious lot of documentation in a function that is not exported.
 
 *source:*
 [Brim/src/permutations.jl:38](file:///home/tpoisot/.julia/v0.3/Brim/src/permutations.jl)
+

doc/index.md

@@ -4,6 +4,7 @@
 [![Coverage Status](https://coveralls.io/repos/PoisotLab/Brim.jl/badge.svg?branch=master)](https://coveralls.io/r/PoisotLab/Brim.jl?branch=master)
 [![codecov.io](http://codecov.io/github/PoisotLab/Brim.jl/coverage.svg?branch=master)](http://codecov.io/github/PoisotLab/Brim.jl?branch=master)
 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.16579.svg)](http://dx.doi.org/10.5281/zenodo.16579)
+[![Documentation Status](https://readthedocs.org/projects/brimjl/badge/?version=latest)](https://readthedocs.org/projects/brimjl/?badge=latest)
 
 Various ways to optimize the modularity of bipartite networks using BRIM in
 `Julia`.

src/draw_matrix.jl

@@ -1,3 +1,7 @@
+"""
+Takes a `Modular` object, and reorder it by module. The row / columns of `A` and
+`S` are modified.
+"""
 function reorder_by_module!(M::Modular)
   nA = zeros(M.A)
   nS = zeros(M.S)
@@ -26,24 +30,35 @@ function reorder_by_module!(M::Modular)
   M.S = nS
 end
 
+"""
+Takes a `Modular` object, and plot it using the *Cairo* driver.
+
+**Keyword arguments:**
+
+- `reorder::Function`, a function to change the order of species (by default, `reorder_by_module!`)
+- `file`: the name of the file to draw in (has to end in `.png`)
+
+Note that the modules are identified by color, using the
+`distinguishable_colors` function from the `Colors` package.
+"""
 function draw_matrix(M::Modular; reorder::Function = reorder_by_module!, file="modular.png")
   reorder(M)
   number_modules = size(M.S)[2]
   module_color = distinguishable_colors(number_modules)
   nbot, ntop = size(M.A)
   width  = 4 + nbot*(10+4)
   height = 4 + ntop*(10+4)
-  ## Initialize device
+  # Initialize device
   c = CairoRGBSurface(width, height)
   cr = CairoContext(c)
   save(cr)
-  ## Background
+  # Background
   set_source_rgba(cr, 1.0, 1.0, 1.0, 1.0)
   rectangle(cr, 0.0, 0.0, float(width), float(height))
   fill(cr)
   restore(cr)
   save(cr)
-  ## Draw the blocks
+  # Draw the blocks
   for top in 1:ntop
     for bot in 1:nbot
       if M.A[bot,top] > 0