To remove just xdot package itself from Debian Unstable (Sid) execute on terminal:
sudo apt-get remove xdot
Uninstall xdot and it's dependent packages
To remove the xdot package and any other dependant package which are no longer needed from Debian Sid.
sudo apt-get remove --auto-remove xdot
If you also want to delete configuration and/or data files of xdot from Debian Sid then this will work:
sudo apt-get purge xdot
To delete configuration and/or data files of xdot and it's dependencies from Debian Sid then execute:
sudo apt-get purge --auto-remove xdot
More information about apt-get remove
apt-get remove is identical to install except that packages are removed instead of installed. Note that removing a package leaves its configuration files on the system. If a plus sign is appended to the package name (with no intervening space), the identified package will be installed instead of removed.