plotProfile not plotting single image from multiple inputs

20 views
Skip to first unread message

Rebekah Rashford

unread,
Dec 17, 2019, 3:42:25 PM12/17/19
to deep...@googlegroups.com
Hello,

My name is Rebekah Rashford and I am a graduate student working with the plotProfile tool on Princeton Genomics instance of Galaxy. I am currently having trouble plotting a single image that comprises of the information from 2 computeMatrix files. Each time I select "Yes" for "Make one plot per group of regions" I still get two separate output images for each input. Is there another parameter I need to set to get both graphs onto the same plot? 

Thank you so much,
Rebekah Rashford



------------------------------------------------
Rebekah Rashford
Peña Lab
Office: 176G

Devon Ryan

unread,
Dec 18, 2019, 2:20:00 AM12/18/19
to Rebekah Rashford, deepTools
Hi Rebekah,

Setting `yes` there should be all that's needed. Is this the same plot
you get if you select `no`?

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
> --
> You received this message because you are subscribed to the Google Groups "deepTools" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to deeptools+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/CAAG7EJLHcYwkn%2BMLJ6H%3DZsC_KEL5E2o4DqzG9Rp0dGjhE_%3DVqQ%40mail.gmail.com.

Rebekah Rashford

unread,
Dec 18, 2019, 2:02:42 PM12/18/19
to Devon Ryan, deepTools
Also, so sorry but one more thing! The same issue has come up for plotHeatmap as I tried to plot both of my graphs on the same plot. Would you recommend importing my matrices into python to plot there?

All the best,
Rebekah



------------------------------------------------
Rebekah Rashford
Peña Lab
Office: 176G

Devon Ryan

unread,
Dec 18, 2019, 2:49:07 PM12/18/19
to Rebekah Rashford, deepTools
This sounds like a bug in the Galaxy wrapper, since this works fine on
the command line. Which Galaxy server are you using and do you know
what version of deepTools you're using on it?

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/CAAG7EJLc-2kzsJX8XTMhViC%3D4RCmWKMJGX2Z7rOz-G7k4Sx%3D6w%40mail.gmail.com.

Rebekah Rashford

unread,
Dec 18, 2019, 2:50:49 PM12/18/19
to Devon Ryan, deepTools
I am using the Princeton Genomics Galaxy server, and the version says it's version number 3.1.2.0.0

Thanks you,
Rebekah




------------------------------------------------
Rebekah Rashford
Peña Lab
Office: 176G

Devon Ryan

unread,
Dec 19, 2019, 4:14:49 AM12/19/19
to Rebekah Rashford, deepTools
We're looking into this off-list with the person we think is running
this server. At least on our local Galaxy instance this option is
working correctly with deepTools 3.1.2

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/CAAG7EJ%2BgsZ5HikQ6WSxyE8NQ40cUgRg9LAB55yPmp%3Dwz_VDYzg%40mail.gmail.com.

Rebekah Rashford

unread,
Dec 19, 2019, 8:48:35 AM12/19/19
to Devon Ryan, deepTools
Awesome! I'll try it with that version until I hear back from you, then.

Thank you again,
Rebekah



------------------------------------------------
Rebekah Rashford
Peña Lab
Office: 176G

Rebekah Rashford

unread,
Dec 19, 2019, 9:02:33 AM12/19/19
to Devon Ryan, deepTools
Oops, sorry. I meant to say I will try with an earlier version. But I just did and it still didn't work, so I will wait to hear back from you!

Rebekah



------------------------------------------------
Rebekah Rashford
Peña Lab
Office: 176G

Rebekah Rashford

unread,
Jan 8, 2020, 3:03:35 PM1/8/20
to Devon Ryan, deepTools
Hi Devon,

Happy New Year! I am still having trouble with plotting two plots on top of one another using the plotProfile version 3.2.1 tool in Galaxy. I tried reverting to an earlier version (3.1) and it didn't work. Should I try downloading the matrix and creating the plot through coding? Are the matrices compatible with Jupyter notebooks for Python?

Thank you so much,
Rebekah

------------------------------------------------
Rebekah Rashford | Peña Lab
Princeton Neuroscience Institute | Office: 176G
Princeton University

Devon Ryan

unread,
Jan 8, 2020, 3:39:57 PM1/8/20
to Rebekah Rashford, deepTools
You can also just run plotProfile locally rather than in Galaxy.
deepTools is written in python, so you could also just use its API in
a jupyter notebook.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/CAAG7EJKLyuxvY%2BK-c41ZuZ9KtucUjAq4%2B-wuBreMrtLxMMfJ_Q%40mail.gmail.com.

Rebekah Rashford

unread,
Jan 8, 2020, 3:42:49 PM1/8/20
to Devon Ryan, deepTools
Awesome--thank you so much for all of your help!




------------------------------------------------
Rebekah Rashford | Peña Lab
Princeton Neuroscience Institute | Office: 176G
Princeton University

Reply all
Reply to author
Forward
0 new messages