Empty y-axis when plotting deeptools computeMatrix mat file.

Question

[anatolybridge]

I generated the image using plotProfile deeptools command and it has no scale on the y-axis although as far as I know it should have one by default, or otherwise this chart is quite meaningless.

I would like the y-axis to have a scale of some sort, like the one illustrated in the example on the plotProfile deeptools page, so that I could compare the two lines displayed by the graph.

So, is there a plotProfile command that would take the scale used by the program to generate the chart and put it on the y-axis? Also, how come that my chart doesn't show the y-axis scale by default, is it because something's wrong with the bedgraph file I converted into bw that I then inputted into the computeMatrix?

The bigwig file used to plot this chart was derived from a bedGrpah file that looked like this:

Thank you very much for the time you spend to read this and understand my problem!

Edit: The commands I used to get this chart:

computeMatrix reference-point -S GSM1668531_TET2_ChIP.ucsc.bw -R tl.bed bg_0.bed -o matrix_bg_0.mat.gz

plotProfile matrix_bg_0.mat.gz -o tl_and_bg_0.png

[ATpoint]

Please show relevant commands and the plot. Brief Reminder On How To Ask A Good Question

[ATpoint]

Your uploaded images do not work properly, please use something like Imgur as image hoster. The current one you use does not behave well on Biostars.

[anatolybridge]

Done. Sorry, I was able to see the pics even when logged out, so I assumed everything was working fine.

[Ram]

If you used the website imggmi or something similar with CloudFlare DDoS protection, whether or not a user sees the image is dependent on how long they remain on the webpage containing the post. Let's say it takes 5 seconds to load the image - this means the user needs to stay on the page for longer than 5 seconds and then refresh the page so the browser (that now has access to the image) can load the image.

Given that the user cannot differentiate between a broken link and a DDoS-protected time-delayed link, they will in all probability move on from the post instead of doing this complicated dance.

[anatolybridge]

Wow, never would have thought of it myself. Thank you for the clarification, I've changed my image hoster to imgur, hope now everything works all right.

Answer 1

[anatolybridge]

I don't know whether it is accepted here to answer your own questions, but I think I've found the cause and solution of the problem and I want to share my findings.

Problem: The empty y-axis appeared to be the bug reported on the plotProfile page.

Solution: I uninstalled anaconda 2019.07, and installed an older version (2019.03) from the archive, then I reinstalled deepTools, and as a result I generated the graph with a 'normal' y-axis:

[Ram]

To mark your question as Solved, please accept an answer that solves it. You can accept multiple answers (if they all solve the question). You can also accept your own answer.

[ATpoint]

Accepted and encouraged, thanks for following up!