Command-line usage
Run d4-plot --help or d4-plot-server --help for all options. Paths may be absolute or relative to the current directory.
Desktop
d4-plot sample.d4
d4-plot sample1.d4 sample2.d4
d4-plot --region chr1:1,000,000-2,000,000 sample.d4
d4-plot --locale ja sample.d4
Regions use 1-based, inclusive coordinates. chr1:100 selects one base; chr1 selects the chromosome. --locale overrides the saved language for one run.
Browser server
d4-plot serve and d4-plot-server accept the same options:
d4-plot serve --genome hg38 --open sample.d4
d4-plot-server --genome hg38 --open
d4-plot-server --reference reference.fa --reference-index reference.fa.fai sample.d4
The server prints a token URL, binds to 127.0.0.1, and runs until Ctrl-C. Open the URL on the same computer; do not share it. --open launches the browser, but failure to launch it does not stop the server.
Choose at most one reference mode:
| Option | Reference |
|---|---|
--genome ID |
Public IGV preset, such as hg38. |
--reference PATH |
Local FASTA or IGV genome JSON. FASTA requires a .fai; use --reference-index PATH for a different location. |
--contigs-only |
Names and lengths from D4, without sequence bases. |
With a D4 file and no reference option, the server uses its contigs. Without a D4 file, specify --genome or --reference. A D4 contig dictionary does not establish the source assembly. Public presets fetch reference data from public hosts; use a local FASTA/FAI to keep reference access local. A JSON reference must point to files accessible from the browser.
| Option | Use |
|---|---|
--region REGION |
Initial locus, such as chr1:100-200. |
--locale LOCALE |
Browser language. |
--port PORT |
Loopback port; 0 selects an available port. |
--open |
Open the URL after startup. |
On Windows, run d4-plot-server in a terminal to copy the URL. In the macOS bundle, it is at d4-plot.app/Contents/MacOS/d4-plot-server. See IGV integration for track and reference behavior.