plotProfile not plotting single image from multiple inputs
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Rebekah Rashford
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Dec 17, 2019, 3:42:25 PM12/17/19
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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?
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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
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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?
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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
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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
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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?
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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