odgi layout¶
use SGD to make 2D layouts of the graph
SYNOPSIS¶
odgi layout [-i, –idx=FILE] [-o, –out=FILE] [OPTION]…
DESCRIPTION¶
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.
OPTIONS¶
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.