export images as png by running a script

[Dima]

Hello,

I am tryign to automate image export out of the cytscape - was wonderign if I can create a png out of the network with top resolution and dpi by just runnign a script file?

Dima

[Alex Pico]

Hi Dima,

Using the RCy3 package, you have the exportImage() function, which can produce vector graphics (like SVG and PDF) or raster graphics at any resolution you want (like PNG):

https://bioconductor.org/packages/release/bioc/html/RCy3.html

Try the overview vignette: https://bioconductor.org/packages/release/bioc/vignettes/RCy3/inst/doc/Overview-of-RCy3.html 

Here are more examples of the exportImage() options for large PNGs:

exportImage(‘my_image_file', 'PNG', zoom=200) #.png scaled by 200%

exportImage(‘my_image_file', 'PNG', width=1500) #.png scaled to a width of 1500 pixels 

 - Alex

[Dima]

Thank you for your kidn reply - do I need to have the r isntalled to run this script? I am using high level automation macro (netork automation Automate)  - can I just rung a script file to do this from inside the Cytoscape?

[Alex Pico]

Sure. I previously shared an R package solution, but you can also do this in Cytoscape directly using “Commands”.

To test out command syntax, open Tools>Command Line Dialog and then type ‘help view export’ and you’ll see the same options as in R:

Exports the current view to a graphics file and returns the path to the saved file. PNG and JPEG formats have options for scaling, while other formats only have the option 'exportTextAsFont'. For the PDF format, exporting text as font does not work for two-byte characters such as Chinese or Japanese. To avoid corrupted texts in the exported PDF, please set false to 'exportTextAsFont' when exporting networks including those non-English characters.

view export arguments:

Height=<Double>:

The height of the exported image. Valid only for bitmap formats, such as PNG and JPEG.

options=<ListSingleSelection (JPEG (*.jpeg, *.jpg)|PDF (*.pdf)|PNG (*.png)|PostScript (*.ps)|SVG (*.svg))>:

The format of the output file.

OutputFile=<File>:

The path name of the file where the view must be saved to. By default, the view's title is used as the file name.

Resolution=<ListSingleSelection (72|100|150|300|600)>:

The resolution of the exported image, in DPI. Valid only for bitmap formats, when the selected width and height 'units' is ```inches```. The possible values are: ```72``` (default), ```100```, ```150```, ```300```, ```600```.

Units=<ListSingleSelection (pixels|inches)>:

The units for the 'width' and 'height' values. Valid only for bitmap formats, such as PNG and JPEG. The possible values are: ```pixels``` (default), ```inches```.

Width=<Double>:

The width of the exported image. Valid only for bitmap formats, such as PNG and JPEG.

Zoom=<BoundedDouble (0.0<=100.0<=500.0)>:

The zoom value to proportionally scale the image. The default value is ```100.0```. Valid only for bitmap formats, such as PNG and JPEG.       

The command script can be run in this interface or as a script file. The equivalent examples as provided before would look like this:

view export OutputFile=my_image_file.png options=PNG Zoom=200

view export OutputFile=my_image_file2.png options=PNG Width=1500

 - Alex

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[Dima Chernovolov]

Fantastic Alex  - there are two options in image export window - DPI (shoudl eb set to 600) and zoom factor (shoudl be 500%) - can you help me woth this command line?

I can just enter it in command ine editor and run right?

Thats soudns closer to my automation goal.

Dima

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[Alex Pico]

Yes! That is how you do it. Give it a try and let me know what does not work.

 - Alex

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[Dima Chernovolov]

I entered this line in Command Line dialog - pasted endter and it did nto show any response

view export OutputFile=my_image_file.png options=PNG Zoom=200

can you pls check

[Dima Chernovolov]

when I type help view export and press enter - it also shows nothing((

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[Alex Pico]

You’ll need the latest version of Cytoscape. Again, version 3.2.1 is very very outdated.

 - Alex

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[Dima]

Thank you Alex - I will instal the new version now - can you please give me the code to eport image as png with 500% zoom factor and PDI of 600?

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[Dima]

I was able to export an image withe a script!!!!  (dancing) I also wanted to ask if there is a way to force overwirite exisiting image? so that no prompt is shown?

[Alexander Pico]

Unfortunately, no there is not. 

 - Alex

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