Peel the beets and cut into wedges. Keep red beets separate from the others.
In a medium bowl, toss the non-red beets with half the olive oil, thyme sprigs, salt and pepper until coated with the oil.
Spread the red beets out on one side of a baking sheet.
Toss the red beets with the rest of the olive oil, thyme sprigs, salt and pepper. Spread on the same baking sheet, separately from the others and cover with foil.
Roast in the oven for 30-40 minutes until soft when pierced with a fork.
Remove from the oven, take off the foil. Remove the thyme sprigs.
While the beets are cooking, in a small bowl, mix the balsamic vinegar with the salt until dissolved. Whisk in the olive oil.
In a medium bowl, gently toss the beets, tomatoes, arugula and pea shoots together with the balsamic vinaigrette.
Serve on plates garnished with the nasturtium flowers and fresh pepper.