odgi layout
Establish 2D layouts of the graph using path-guided stochastic gradient descent (the graph must be sorted and id-compacted).
SYNOPSIS
odgi layout [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
DESCRIPTION
The odgi layout command computes 2D layouts of the graph using path-guided stochastic gradient descent (PG-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
MANDATORY OPTIONS
-i, --idx=FILE
Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
Files IO
-o, --out=FILE
Write the layout coordinates to this FILE in .lay binary format.
-T, --tsv=FILE
Write the layout in TSV format to this FILE.
-X, --path-index=FILE
Load the path index from this FILE so that it does
not have to be created for the layout calculation.
-C, --temp-dir=PATH
Directory for temporary files.
-f, --path-sgd-use-paths=FILE
Specify a line separated list of paths to sample from for the on the fly term generation process in the path guided 2D SGD (default: sample from all paths).
Layout Initialization Options
-N, --layout-initialization=STRING
Specify the layout initialization mode:
d) Node rank in X and gaussian noise in Y (default).
r) Uniform noise in X and Y in the order of the graph length.
u) Node rank in X and uniform noise in Y.
g) Gaussian noise in X and Y
h) Hilbert curve in X and Y.
PG-SGD Options
-G, --path-sgd-min-term-updates-paths=N
Minimum number of terms N to be updated before a new path guided 2D SGD iteration with adjusted learning rate eta starts
, expressed as a multiple of total path length (default: 10).
-U, --path-sgd-min-term-updates-nodes=N
Minimum number of terms N to be updated before a new path guided 2D SGD iteration with adjusted learning rate
eta starts, expressed as a multiple of the number of nodes (default: argument is not set, the default of -G=[N],
path-sgd-min-term-updates-paths=[N] is used.
-j, --path-sgd-delta=N
The threshold of the maximum displacement N approximately in bp at which to stop path guided 2D SGD (default: 0).
-g, --path-sgd-eta=N
The final learning rate N for path guided 2D SGD model (default: 0.01).
-v, --path-sgd-eta-max=N
The first and maximum learning rate N for path guided 2D SGD model (default: squared longest path length).
-a, --path-sgd-zipf-theta=N
The theta value N for the Zipfian distribution which is used as the sampling method for the second node of one term in
the path guided 2D SGD model (default: 0.99).
-x, --path-sgd-iter-max=N
The maximum number of iterations N for the path guided 2D SGD model (default: 30).
-F, --path-sgd-iteration-max-learning-rate=N
Specify the iteration N where the learning rate is max for path guided 2D SGD model (default: 0).
-k, --path-sgd-zipf-space=N
The maximum space size N of the Zipfian distribution which is used as the sampling method for the second node of one
term in the path guided 2D SGD model (default: max path lengths).
-I, --path-sgd-zipf-space-max=N
The maximum space size N of the Zipfian distribution beyond which quantization occurs (default: 1000).
-l, --path-sgd-zipf-space-quantization-step=N
The size of the quantization step N when the maximum space size of the Zipfian distribution is exceeded (default: 100).
-u, --path-sgd-snapshot=STRING
Set the prefix STRING to which each snapshot layout of a path guided 2D SGD iteration should be written to (default: NONE).
Threading
-t, --threads=N
Number of threads to use for parallel operations.
Processing Information
-P, --progress
Write the current progress to stderr.
Program Information
-h, --help
Print a help message for odgi layout.