odgi viz¶

variation graph visualizations

SYNOPSIS¶

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

DESCRIPTION¶

The odgi viz(1) command can produce a linear, static visualization of an odgi variation graph. It can aggregate the pangenome into bins and directly renders a raster image. The binning level can be specified in input or it is calculated from the target width of the PNG to emit. Can be used to produce visualizations for gigabase scale pangenomes. For more information about the binning process, please refer to odgi bin.

OPTIONS¶

Graph Files IO¶

-i, –idx=FILE

File containing the succinct variation graph to convert from. The file name usually ends with .og.

-o, –out=FILE

Write the visualization in PNG format to this file.

Visualization Options¶

-x, –width=N

Set the width in pixels of the output image.

-y, –height=N

Set the height in pixels of the output image.

-P, –path-height=N

The height in pixels for a path.

-X, –path-x-padding=N

The padding in pixels on the x-axis for a path.

-R, –pack-paths

Pack all paths rather than displaying a single path per row.

-L, –link-path-pieces=FLOAT

Show thin links of this relative width to connect path pieces.

-A, –alignment-prefix=STRING

Apply alignment related visual motifs to paths which have this name prefix. It affects the [-S, –show-strand] and [-d, –change-darkness] options.

-S, –show-strand

Use red and blue coloring to display forward and reverse alignments. This parameter can be set in combination with [-A, –alignment-prefix=STRING].

-z, –color-by-mean-inversion-rate

Change the color respect to the node strandness (black for forward, red for reverse); in binned mode (-b, –binned-mode), change the color respect to the mean inversion rate of the path for each bin, from black (no inversions) to red (bin mean inversion rate equals to 1).

-s, –color-by-prefix

Colors paths by their names looking at the prefix before the given character C.

Intervals selection¶

-r, –path-range

Nucleotide range to visualize: STRING=[PATH:]start-end. \*-end for [0,end]; start-* for [start,pangenome_length]. If no PATH is specified, the nucleotide positions refer to the pangenome’s sequence (i.e., the sequence obtained arranging all the graph’s node from left to right).

Paths selection¶

-p, –paths-to-display

List of paths to display in the specified order; the file must contain one path name per line and a subset of all paths can be specified.

Path names visualization Options¶

-H, –hide-path-names

Hide the path names on the left of the generated image.

-C, –color-path-names-background

Color path names background with the same color as paths

-c, –max-num-of-characters

Maximum number of characters to display for each path name (max 128 characters). The default value is the length of the longest path name (up to 32 characters).

Binned Mode Options¶

-b, –binned-mode

The variation graph is binned before its visualization. Each pixel in the output image will correspond to a bin. For more information about the binning process, please refer to odgi bin.

-w, –bin-width=N

The bin width specifies the size of each bin in the binned mode. If it is not specified, the bin width is calculated from the width in pixels of the output image.

-g, –no-gap-links

We divide links into 2 classes:

the links which help to follow complex variations. They need to be drawn, else one could not follow the sequence of a path.
the links helping to follow simple variations. These links are called gap-links. Such links solely connecting a path from left to right may not be relevant to understand a path’s traversal through the bins. Therefore, when this option is set, the gap-links are not drawn in binned mode.

-m, –color-by-mean-coverage

Change the color respect to the mean coverage of the path for each bin, from black (no coverage) to blue (max bin mean coverage in the entire graph).

Gradient Mode (also known as Position Mode) Options¶

-d, –change-darkness

Change the color darkness based on nucleotide position in the path. When it is used in binned mode, the mean inversion rate of the bin node is considered to set the color gradient starting position: when this rate is greater than 0.5, the bin is considered inverted, and the color gradient starts from the right-end of the bin. This parameter can be set in combination with [-A, –alignment-prefix=STRING].

-l, –longest-path

Use the longest path length to change the color darkness.

-u, –white-to-black

Change the color darkness from white (for the first nucleotide position) to black (for the last nucleotide position).

Program Information¶

-h, –help

Print a help message for odgi viz.