Question: ChipSeeker Heatmap (y-axis)?
0
gravatar for dthaper
22 months ago by
dthaper10
dthaper10 wrote:

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.

chipseeker chip-seq • 749 views
ADD COMMENTlink modified 20 months ago by Rashedul Islam350 • written 22 months ago by dthaper10

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

ADD REPLYlink written 22 months ago by Rashedul Islam350

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.

ADD REPLYlink written 22 months ago by dthaper10

I added the answer below.

ADD REPLYlink modified 20 months ago • written 20 months ago by Rashedul Islam350
0
gravatar for dthaper
21 months ago by
dthaper10
dthaper10 wrote:

anyone able to help with this?

ADD COMMENTlink written 21 months ago by dthaper10
0
gravatar for Rashedul Islam
20 months ago by
Canada
Rashedul Islam350 wrote:

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.

ADD COMMENTlink written 20 months ago by Rashedul Islam350
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