odgi viz

Visualize a variation graph in 1D.


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


The odgi viz 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.



-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!
-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 (default: 1500).
-y, --height=N
Set the height in pixels of the output image (default: 500).
-a, --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.
-n, --no-path-borders
Don't show path borders.
-b, --black-path-borders
Draw path borders in black (default: draw path borders in white).
-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).
-N, --color-by-uncalled-bases
Change the color with respect to the uncalled bases of the path for each bin, from black (no uncalled bases) to green (all uncalled bases).
-s, --color-by-prefix=CHAR
Color paths by their names looking at the prefix before the given character CHAR.
-M, --prefix-merges=FILE
Merge paths beginning with prefixes listed (one per line) in FILE.
-I, --ignore-prefix=PREFIX
Ignore paths starting with the given PREFIX.

Intervals Selection Options

-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).

Path Selection Options

-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 Viz 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=N
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

-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.
-m, --color-by-mean-depth
Change the color with 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).
-B, --colorbrewer-palette=SCHEME:N
Use the colorbrewer palette specified by the given SCHEME, with the number of levels N. Specifiy 'show' to see available palettes.
-G, --no-grey-depth
Use the colorbrewer palette specified for < 0.5x and ~1x coverage bins (default: these bins are light and neutral grey).

Gradient 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).

Compressed Mode Options

-O, --compressed-mode
Compress the view vertically, summarizing the path coverage across all paths displaying the information using only one path COMPRESSED_MODE. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Alternatively, one can enter a colorbrewer palette via -B, --colorbrewer-palette=SCHEME:N.


-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 viz.