Alignment
---------

Alignment of hierarchical and event-related gene collinearity.

.. rubric:: Parameters

.. tabularcolumns:: column spec

================= ========================================================================
Parameters        Standards and instructions
----------------- ------------------------------------------------------------------------
blockinfo         Type: **file**  |    Default: **-**
                     
                  Output result of parameter `bi`
----------------- ------------------------------------------------------------------------
colors            Type: { **color1,color2,color3,--** }    Default: **red,blue,green**
 
                  Set multiple sets of colors based on grouping, split with a comma.
----------------- ------------------------------------------------------------------------
position          Type: {**order**, **start** , **end** }  |  Default: **order**

                  The position of the gene corresponds to the gff file.
----------------- ------------------------------------------------------------------------
blockinfo_reverse Type: **bool**   |    Default: **false**

                  The two species aligned swap positions..
----------------- ------------------------------------------------------------------------
figsize           Type: **int,int** |  Default: **10,10**

                  Control the proportion of the size of the saved picture.
----------------- ------------------------------------------------------------------------
savefile          Type: **file**   |  Default: \* **.csv**
                    
                  Result file.
----------------- ------------------------------------------------------------------------
markersize        Type: **float**   | Default: **0.5**

                  The size of the point in the plot.  
----------------- ------------------------------------------------------------------------
savefig           Type: {\*. **png**, \*. **pdf**, \*. **svg**}  |  Default: \*. **png**

                  Save pictures support png, pdf, svg formats.
================= ========================================================================


Use command to enter the folder ``wgdi -a ? > align.conf`` Take out the parameter file.

.. code-block:: python

   [alignment]
   gff1 =  gff1 file
   gff2 =  gff2 file
   lens1 = lens1 file
   lens2 = lens2 file
   genome1_name =  Genome1 name
   genome2_name =  Genome2 name
   markersize = 0.5
   position = order
   colors = red,blue,green
   figsize = 10,10
   savefile = savefile(.csv)
   savefig= save image
   blockinfo = block information file
   blockinfo_reverse = false

.. rubric:: Quick start

After the parameters are modified properly, then run ``wgdi -a total.conf`` 

.. rubric:: Example

The original results are easily accessible at `wgdi-example <https://github.com/SunPengChuan/wgdi-example>`_

.. image :: _static/soin164s_oda165s_ono163s.alignment.png
   :align: left