However, I am trying to demonstrate that motifs for different transcription factors will be found in the same peaks. Is there a way to use the functions from genomation or another tool to do this?
To be a little more clear, the plot I am referring to shows where in each peak the CTCF motif occurs, in green. I would like to add two more transcription factors to a plot like this, in different colors.
You can't show three different motif occurrence matrices on the same heatmap with different color codings for each motif using genomation. However, you can show those in three separate heatmaps. The problem with showing all three motif position sets in one heatmap is the positions where two or more motifs overlap. You have to use transparent cells and depending on how much overlap there is, things might look ugly.
If you can figure out a way to show three different motif sets on the same heatmap you can still use patternMatrix() function to get the matrices for motif occurrences.