There are multiple options:
1) you can use nodeClasses in combination with showAll mode - by adding a className parameter to the nodes and by setting up nodeClasses you can control which nodes are visible and which are not
2) you can also use nodeStyleFunction with combination of showAll navigation mode and then you can selectively change the style of the nodes that you want to show
3) you can use custom dataFunction method and before passing the data to the chart, you can go through the nodes and pick the initial nodes upon the initial load.
So, there are many options to address your situation and to provide the ideal solution, you would need to talk about the end result and overall UX and planned features.