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Every flag the command has and every reader behind it, over the files on the left. The region string, the coordinate conventions, the counts and every refusal are what the terminal gives, because it is the same code: the grammar lives in the library and takes a closure that answers with a file's text, so a shell hands it a disk and this page hands it the editor.

The controls under the figure belong to the example. They are not the same for every one, because the figures are not the same thing: a window to slide is what a signal over a chromosome has and a tanglegram has not, and a tanglegram says so rather than offering a slider that would mean nothing. Every control is a flag, and turning one rewrites that flag in the command above, which is the thing that decides.

A window is bounded by the stretch its own files cover, so it cannot be put somewhere there is nothing to draw.

Interactive adds the pointer to that: drag the figure to pan, and scroll to zoom once it has focus. Nothing is transformed or scaled, and nothing is cached: every frame is a figure karyon drew, at that region, from those files.

The pane supplies two things the command does not: the width to draw at, and the dark theme when the page is dark. Writing --width or --theme in the box overrules both, since the command is the thing that decides.

Two things are a terminal's and are answered as text here. - for standard input, because nothing is piped into a page. And --help, which is the command line guide written out.