I use dot, and manually position everything, then use the neato -n2 option to render:

`dot -T ${format} -n${n} ${verbose>1?"-v ":""}-Goverlap-true -Gsplines=false -Kneato -o "${ output }" "${ input }"`

this still doesn't do subgraphs well,

so I sometime do the 'groups' in a separate document, then composite the layers with image magick

`magick composite ${verbose>1?"-verbose ":""}-gravity NorthWest "${a}" "${b}" "${png_output}"`;