odgi layout

use SGD to make 2D layouts of the graph


odgi layout [-i, –idx=FILE] [-o, –out=FILE] [OPTION]…


The odgi layout(1) command computes 2D layouts of the graph using stochastic gradient descent (SGD). The input graph must be sorted and id-compacted. The algorithm itself is described in Graph Drawing by Stochastic Gradient Descent. The force-directed graph drawing algorithm minimizes the graph’s energy function or stress level. It applies SGD to move a single pair of nodes at a time.


Graph Files IO

-i, –idx=FILE
File containing the succinct variation graph to layout. The file name usually ends with .og.
-o, –out=FILE
Write the rendered layout in SVG format to FILE.

SGD Options

-m, –iter-max=N
The maximum number of iterations to run the layout. Default is 30.
-p, –n-pivots=N
The number of pivots for sparse layout. Default is 0 leading to a non-sparse layout.
-e, –eps=N
The learning rate for SGD layout. Default is 0.01.

SVG Options

-x, –x-padding=N
The padding between the connected component layouts. Default is 10.0.
-R, –render-scale=N
SVG scaling Default is 5.0.

Processing Information

-d, –debug
Print information about the components to stdout.

Program Information

-h, –help
Print a help message for odgi layout.