odgi draw

Draw previously-determined 2D layouts of the graph with diverse annotations.

SYNOPSIS

odgi draw [-i, --idx=FILE] [-c, --coords-in=FILE] [-p, --png=FILE] [OPTION]…

DESCRIPTION

The odgi draw command draws previously-determined 2D layouts of the graph with diverse annotations.

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!

-c, --coords-in=FILE

Read the layout coordinates from this .lay format FILE produced by odgi layout.

Files IO

-T, --tsv=FILE

Write the TSV layout plus displayed annotations to this FILE.

-s, --svg=FILE

Write an SVG rendering to this FILE.

-p, --png=FILE

Write a rasterized PNG rendering to this FILE.

-X, --path-index=FILE

Load the path index from this FILE.

Visualization Options

-H, --png-height=N

Height of PNG rendering (default: 1000).

-E, --png-border=N

Size of PNG border in bp (default: 10).

-C –color-paths

Color paths (in PNG output).

-R, --scale=N

Image scaling (default 1.0).

-B, --border=N

Image border (in approximate bp) (default 100.0).

-w, --line-width=N

Line width (in approximate bp) (default 0.0).

-S, --path-line-spacing=N

Spacing between path lines in PNG layout (in approximate bp) (default 0.0).

-b, --bed-file=FILE

Color the nodes based on the input annotation in the given BED FILE. Colors are derived from the 4th column, if present, else from the path name. If the 4th column value is in the format 'string#RRGGBB', the RRGGBB color (in hex notation) will be used.

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Print information about the operations and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi draw.