Take microaray data for example. If you've done an experiment with four time points; hours 1, 2, 4, and 8. The columns of your data set are the time points and the rows are the individual genes (see below).
|# Hour 1||Hour 2||Hour 4||Hour 8|
Loading the above data set into CompClustTk and then running a Trajectory Summary plot (see section 3.5.2), you would see that the first gene's trajectory (vector) starts high and gets lower of the four time points. Formatting your data into a tab delimited formated similar to the one shown above will allow you to load your own data sets into CompClustTk.