If I understand your question correctly you can use an application filter for the Transaction Flow dashlet. Open the Transaction Flow Dashlet from the cockpit from the profile where the application is being monitored and at the top of Dynatrace Client below the menu options pick the second funnel icon. From here you can pick your desired application from the application list that have been auto-discovered or user defined. You can also right click on the Transaction Flow Dashlet name and select edit filter and pick from the applications tab. Once you have your desired settings you can save this a dashboard.
Check out this link Usage of Dashboards and scroll to the "Filter Dashboard and Dashlet Data" section.