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sidhomj / DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
https://sidhomj.github.io/DeepTCR/
MIT License
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Heatmap save to file output blank file #6

Closed hejing3283 closed 5 years ago

hejing3283 commented 5 years ago

DTCRU.HeatMap_Sequences(filename='Heatmap_Sequences.pdf')

The resulted file is blank.

sidhomj commented 5 years ago

The output must be an image. Not a pdf.

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On Apr 26, 2019, at 11:50 AM, Jing He notifications@github.com<mailto:notifications@github.com> wrote:

DTCRU.HeatMap_Sequences(filename='Heatmap_Sequences.pdf')

The resulted file is blank.

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hejing3283 commented 5 years ago

so it's a png, the tiff is not supported?

sidhomj commented 5 years ago

It may depend on the OS you are using. I think tiff should work on Linux systems. I generally use either eps or png.

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On Apr 26, 2019, at 12:05 PM, Jing He notifications@github.com<mailto:notifications@github.com> wrote:

so it's a png, the tiff is not supported?

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hejing3283 commented 5 years ago

I use macOS and linux. None of them works. Cannot save to eps or png neither.

sidhomj commented 5 years ago

Will look at this later tonight. Sorry for the delay.

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On Apr 26, 2019, at 1:20 PM, Jing He notifications@github.com<mailto:notifications@github.com> wrote:

I use macOS and linux. None of them works. Cannot save to eps or png neither.

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hejing3283 commented 5 years ago

Thanks!

sidhomj commented 5 years ago

hmm. i'm not having a problem saving png or eps images.. are you getting an actual error?

hejing3283 commented 5 years ago

No error at all. Just blank page.

On Apr 26, 2019, at 20:54, John-William Sidhom notifications@github.com wrote:

hmm. i'm not having a problem saving png or eps images.. are you getting an actual error?

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sidhomj commented 5 years ago

with with png? I can't replicate the problem on my end so it's hard to know how to fix it.. can you try running DeepTCR within an IDE like pycharm? as oppose to just from cmd.

hejing3283 commented 5 years ago

I tried .tif, png, off, eps, none of them works. But from Jupyter notebook, it shows up.

Best, Jing

On Apr 26, 2019, at 23:02, John-William Sidhom notifications@github.com wrote:

with with png? I can't replicate the problem on my end so it's hard to know how to fix it.. can you try running DeepTCR within an IDE like pycharm? as oppose to just from cmd.

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sidhomj commented 5 years ago

So it’s only a problem when running DeepTCR from command line?

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On Apr 27, 2019, at 11:15 AM, Jing He notifications@github.com<mailto:notifications@github.com> wrote:

I tried .tif, png, off, eps, none of them works. But from Jupyter notebook, it shows up.

Best, Jing

On Apr 26, 2019, at 23:02, John-William Sidhom notifications@github.com<mailto:notifications@github.com> wrote:

with with png? I can't replicate the problem on my end so it's hard to know how to fix it.. can you try running DeepTCR within an IDE like pycharm? as oppose to just from cmd.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

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hejing3283 commented 5 years ago

The heatmap shows up in notebook, but cannot be saved to a file no matter how I run it.

Best, Jing

On Apr 27, 2019, at 11:17, John-William Sidhom notifications@github.com wrote:

So it’s only a problem when running DeepTCR from command line?

Sent from my iPhone

On Apr 27, 2019, at 11:15 AM, Jing He notifications@github.com<mailto:notifications@github.com> wrote:

I tried .tif, png, off, eps, none of them works. But from Jupyter notebook, it shows up.

Best, Jing

On Apr 26, 2019, at 23:02, John-William Sidhom notifications@github.com<mailto:notifications@github.com> wrote:

with with png? I can't replicate the problem on my end so it's hard to know how to fix it.. can you try running DeepTCR within an IDE like pycharm? as oppose to just from cmd.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/sidhomj/DeepTCR/issues/6#issuecomment-487294081, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGVMZTAWEDHSVR3GFGGSCLDPSRUUXANCNFSM4HIWX2KQ. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

hejing3283 commented 5 years ago

I installed pillow and set the backend as 'pdf' by the following scripts, it works now.

import matplotlib matplotlib.use("pdf")