Ignore invisible items for dot layout

[XiaoMigros]

Resolves: #9941

• [x] I signed the CLA
• [x] The title of the PR describes the problem it addresses
• [x] Each commit's message describes its purpose and effects, and references the issue it resolves
• [ ] If changes are extensive, there is a sequence of easily reviewable commits
• [x] The code in the PR follows the coding rules
• [x] There are no unnecessary changes
• [x] The code compiles and runs on my machine, preferably after each commit individually
• [x] I created a unit test or vtest to verify the changes I made (if applicable)

[RomanPudashkin]

@XiaoMigros please rebase

[Jojo-Schmitz]

Urgs, something bad happened, 840 commits???

[XiaoMigros]

rebase seems to have gone wrong, will fix~