:tocdepth: 3

.. _guppy_fat:

===
fat
===

`fat` makes trees with edges fattened in proportion to the number of reads.

::

  usage: fat [options] placefile[s]

Options
=======

-o  Specify the filename to write to.
--out-dir  Specify the directory to write files to.
--prefix  Specify a string to be prepended to filenames.
--point-mass  Treat every pquery as a point mass concentrated on the highest-weight placement.
--pp  Use posterior probability for the weight.
-c  Reference package path.
--min-fat  The minimum branch length for fattened edges (to increase their visibility). To turn off set to 0. Default: 0.01
--total-width  Set the total pixel width for all of the branches of the tree. Default: 300
--width-factor  Override total-width by directly setting the number of pixels per unit of thing displayed.
--node-numbers  Put the node numbers in where the bootstraps usually go.
--average  Average all input placefiles together.
--edpl  Specify the maximum EDPL for an EDPL tree.

Details
=======

Given a list of place files, ``--average`` normalizes the mass in each, then
takes the average of those masses to make an appropriately averaged fat tree
for those place files.

Expected Distance between Placement Locations (EDPL) values can be visualized
on the tree by specifying a maximum value for the scale via the ``--edpl``
flag. The scale is represented by 0 EDPL being white, going to red for the
maximum value. When EDPL is above the specified maximum, the branch is colored
yellow. When there are multiple placements on a given edge, their EDPL values
are combined using a weighted average, where the weights are the values of the
ML weight ratio or posterior probability.