I have a polygon shapefile of aggregated commuting journeys that has >10,000 features in it. Each feature has a unique ID. I have a csv file that contains thousands of rows. Each row represents one feature from the shapefile. Each polygon can be represented by numerous rows, where each row is the count of journeys from the original polygon to the destination polygon. I have attached a picture that may better explain what I'm trying to articulate.
You can create an origin destination matrix and plot it in qgis using a plugin flow mapper.
For creating a origin and destination matrix from your data i think you need to reverse the script on this page https://stackoverflow.com/questions/38870319/tableau-reshaping-a-row-with-origin-destination-into-two-separate-origin-and-des, it should look like table given below : The yellow row and column are the nodes for origin and destination.
Save this matrix in tab delimited format without headers as shown below and also you would need a list of nodes with corresponding lat long to plot it on map. In total you need the three files given below :
Headless OD Matrix
You can give names of the points i have kept codes here
The coordinates of the points in longitude(1st column) Latitude(2nd column) format
I think i made everything clear here, if you need any more help feel free to ping me : firstname.lastname@example.org, Urbantalks.in.