To delete objects in the scene you are no longer interested in, such as a heatmap or gene correlation network, use the delete tool. It is found on the Tool side of the menu and is activated by clicking on the "Delete tool" button. The action controller (the controller you clicked on the button with) will turn into the delete tool. A sphere is now seen on the edge of it. Bring the controller inside the object to want to delete and once inside the sphere will turn red and if you click the trigger button the object will be deleted. Unlike the hide tool, the deleted objects can not be brought back so make sure you want to delete them. If you are not sure then use the hide tool instead.

The original graphs can not be deleted but everything else can. Use the hide tool if you want to temporarily remove them.