ChipSeeker Heatmap (y-axis)?

Question

[dthaper]

I was wondering if there is a way to adjust the Y-axis on the Heatmap produced through Chipseeker. I am pulling down a transcription factor with and without its inhibitor. As expected, there are considerably less peaks in the heatmap, however, they are spread out along the same Y-axis and therefore visually inaccurate. The image is linked below!

thanks!

peaks Peak1 is Control and Peak2 is treated.

[Rashedul Islam]

What is the center of the heatmap? Can you rephrase your question?

[dthaper]

The center of the heatmap is transcription start sites. Peaks in the middle is binding at the TSS. Peak 1 has over 10,000 binding sites while Peak 2 has around 700. But since the Y-axis is the same, Peak 2 looks like it has more binding to an un-trained eye. Its hard to present the data this way.

[Rashedul Islam]

I added the answer below.

Answer 1

[dthaper]

anyone able to help with this?

Answer 2

[Rashedul Islam]

They are spread because you plotter around the TSS. To see the difference you are expecting, plot the binding sites around the peak centers of peak1 instead of TSS.