Export PCAo plots

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Beatriz Gil Pulido

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Aug 18, 2016, 12:38:59 PM8/18/16
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Hi, 

I would like to export the graphs generated in the 3D and 2D PCoA scripts. I don't get the way to do it for the 3D ones and for the 2D there is any problem with the format when download the image from the .htlm file output. 

Someone can give me any clue in how to do it?

Thanks. 


Colin Brislawn

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Aug 18, 2016, 12:43:46 PM8/18/16
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Good morning,

Viewing the 3D PCoA plot using the program called Emperor, you can press 'control+p' to open an image of the plot in a new tab. This will be a .png image, which you can save and use in a publication.

Let me know if you can get 'control + p' working for you in Emperor.

Colin

Beatriz Gil Pulido

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Aug 19, 2016, 7:21:43 AM8/19/16
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Hi Colin, 

Once I press `control+p' a print window appears. The only option I can find is to save the file into .pdf format but actually it does not work either. Apparently I cannot get 'control+p' working. 

Bea 

Colin Brislawn

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Aug 19, 2016, 1:31:17 PM8/19/16
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Hello Bea,

Make sure you are pressing 'control + p' and not 'command + p'. On a mac, look for the control key in the bottom left corner of your keyboard. 

This should open a new tab. In this new tab, right click on the background and select 'save as.'

Let me know if that helps,
Colin

Jai Ram Rideout

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Aug 19, 2016, 7:30:49 PM8/19/16
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Hi Bea,

I noticed you also had a question about exporting 2D PCoA plots. Click "Download Figure" below the figure you wish to export, and you'll be prompted to save the file somewhere. It will be saved as a gzipped (.gz) file. Once you extract it, you'll have a .eps file, which is the image file. You can open .eps files in a variety of programs such as Adobe Illustrator or OS X's Preview and convert it to a different file format.

Best,
Jai

Beatriz Gil Pulido

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Aug 22, 2016, 5:32:37 AM8/22/16
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Hello Colin, 

I don't have a mac. I pressed Ctrl+p (at the same time) and a new window appears for printing as it shown in the document I attach in this email. I cannot see where the "save as" is. 

Regards, 

Bea. 


export PCoA plots .docx

Beatriz Gil Pulido

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Aug 22, 2016, 5:46:32 AM8/22/16
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Hi Jai, 

Once I click in "Download Figure" below the figure, I don't have the option to save the file somewhere. Just a window open and ask me to open it or not. If press "open" I cannot open it because of the format (I attached a prtScn) and if clicking "cancel" nothing happens and the file is not saved. 

Bea. 
export 2D plots .docx

Jai Ram Rideout

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Aug 22, 2016, 1:50:43 PM8/22/16
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Hi Beatriz,

For some reason your operating system (Windows) thinks it can open a file ending in .eps.gz using Adobe Acrobat reader. You'll need to install a program that can extract .gz files (such as 7-Zip) and change the file type associations in Windows (e.g. see this guide) so that Windows will use 7-Zip to extract .gz files instead of attempting to open them in Adobe Acrobat reader. You may also need to disassociate .eps files from being opened in Adobe Acrobat reader. Once that is all set up, you should be able to click "Download Figure" and be prompted for a location to save it. Once saved, you can extract it using 7-Zip and view/convert the .eps file using the software of your choice.

I don't use Windows and many of the developers monitoring this forum don't either, so we may be limited in our ability to help you configure Windows. If the above suggestion doesn't work, you may want to contact your IT support to get help with opening .eps.gz files (the issue here isn't specific to QIIME or make_2d_plots.py).

Best,
Jai

Jai Ram Rideout

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Aug 22, 2016, 1:55:22 PM8/22/16
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Hi again Beatriz,

Regarding your Emperor export issue: can you try clicking "Save as SVG" instead? You should be prompted to save the .svg file somewhere, and you can use software (there are many choices on Windows) to view/edit/convert the .svg file into the desired format (e.g. PNG).

Best,
Jai

Beatriz Gil Pulido

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Aug 23, 2016, 8:26:33 AM8/23/16
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Hi Jai, 

Thanks for the advice. I will check it with the tips you gave me or I will contact with the IT support. 

Regarding to your second message, I can safe the 3D plot in svg format but for example the percentage of each axis do not appear. So I think will be better just to do a screenshot with the 3D plots and that is all. I don´t know how to figure out with Emperor in my computer. 

Let see if I can fix about the problem downloading the 2D plots with your tips. 

Thanks, 

Bea. 

Jai Ram Rideout

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Aug 23, 2016, 1:27:59 PM8/23/16
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Hi Beatriz,

That's odd, both SVG and PNG exports don't include the axis labels. I'll contact the Emperor developers to help you with this.

Best,
Jai

Jai Ram Rideout

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Aug 23, 2016, 1:38:41 PM8/23/16
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Hi Beatriz,

I checked with Yoshiki and it is a known issue for SVG and PNG formats. The newest version of Emperor supports this but it isn't compatible with QIIME 1. I think you may need to do a "print screen", save as PDF, and edit/convert it as necessary.

Jai
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