I have been using Cytoscape's EnrichmentMap application for a few weeks, creating GEM files in g:Profiler and visualizing the results with EnrichmentMap. All files I created were working until today. I have generated 8 GEM files for different gene lists in g:Profiler, and 4 of them create the proper network visualization of the graph with labeled circular nodes with edges connecting them when clicking "Build". The other 4 create a network of edges connecting red rectangles that are unlabeled. I am unable to add a picture to Stack Overflow to show this or the GEM files.
I am using Cytoscape 3.8.2 on Windows 10. There are no errors upon creation of the network visualization.
I inspected the GEM files between those that worked and those that did not work, and they did not show any noticeable differences. Any advice would be greatly appreciated and thank you in advance!
Sorry to hear about your issues. Typically, the "red nodes" mean that a Visual Style wasn't loaded. You can easily fix that in Cytoscape by just selecting the style. Take a look for a style called "EM1_Visual_Style" (it might be some other number than 1) and select it. Hopefully that will bring your style back.
-- scooter
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I have created a cytoscape network with a number of crossing and re-crossing edges. It is meant to do this, and I don't wish to reduce the amount of crossing that is occurring.
I would, however, like to be able to determine which edges are on "top" and which are in "back" - in the same way that you would "bring to front" or "send to back" in Powerpoint or Photoshop or any of numerous display programs.
Which style parameter or similar value is used to determine rendering order of edges? Note that I am referring to the edge line itself, and not some annotation.
Thanks much.
Unfortunately, that isn't available in the current release, but Cytoscape 3.9 will include that feature. If you want to try a copy of 3.9 (which isn't nearly ready for production release), you can download it at: https://cytoscape-builds.ucsd.edu/cytoscape-builds/Cytoscape-3.9.0/
-- scooter
I'm still learning to use cytoscape. I have created a compound-target-cancer network and would like to add a key at the bottom, explaining what the different colors of the nodes mean. For example the pink proteins represent cancer-related proteins, the blue proteins represent non-cancer related proteins and the green nodes are my compounds.
Please help...
There is an app under development to provide an easy way to do that. but it probably won't be available until Cytoscape 3.7. In the meantime, you can go to the Style tab, then you'll see a menu tab (four parallel lines), click on that and you'll see a "Create Legend..." option. That will bring up a legend that can be saved as a PNG and add back into your network using a post-processing program.
-- scooter
I'm trying to compare different learning-rate-decays using Tensorflow. Therefore I visualize the cost functions in Tensorboard ('EVENTS'-tab). My problem is that the different plots of the functions are in very similar colors making it hard to compare them. Is there any possibility to change those colors?
Just create different summary writes with different log files for each learning rate. Then launch the tensorboard tool using:
tensorboard --logdir=tag1:/path/to/summary/one,tag2:/path/to/summary/two
There's currently no way to change those colors, but a recent release has made the colors more differentiated. Try updating and seeing if that helps.
This is very far from an actual solution, but in case someone only wants to change the colors for a screenshot in a paper or presentation its a quick workaround:
Open your browser dev tools (F12)
Search for the color code you want to change (the default orange is #ff7043) and replace it with the color you want
As suggested here, creating (and pointing tensorboard to) a symlink of a run's logdir is one workaround to change the color used to plot that run.
What I am ultimately trying to do is to create a grid of images for print that are minor variations of the same thing (different text is all). Looking through online resources I was able to create a script that changes the text and exports all of the images necessary (several hundred). What I am trying to do now is to import all of these images into a new photoshop document and lay them all out in a grid and I can't seem to find any examples of this.
Can anyone point me in the right direction to place a file at a specific coordinate (I'm using CS5 and have the design suite so if there is a way in illustrator to do this quickly...)?
Also, I'm open to other ideas on how to do this (even other programs) easily. It's for labels so the positioning on the sheet has to be pretty precise...
The art layer object has a translate() method that takes delta x and y params. You'll need to open each image, copy it to the target document, get its current location (using artLayer.bounds) and do the math to find the deltas to position it where you want it. Your deltas can be in pixels so you'll get plenty of precision.
Check out your 'JavaScript Scripting Reference' pdf in your Adobe install directory for more details.
Ok I'm marking Anna's response as the answer because though I didn't fully test it, it seems like it should work and answers the original question with jsx. However I'm also leaving my final solution in case anyone else runs across this with the same issue and may prefer this method as well.
What I ended up doing instead is using InDesign. I figured out that it has a grid option that lets you import a number of files and place them all in an equal grid in a single command. This is almost exactly what I was looking for, except that it leaves a small border/margin in between the columns and grids and mine were designed to meet exactly.
I couldn't figure out how to make it not have the border (I have very little experience with InDesign, it may be possible). However I was able to select all my images and scale them uniformly to be the correct size, then I just selected each column and dragged it over to snap to the adjacent column and the same with rows...
I am writing an app that stitches iOS text message screen captures together vertically.
I have the images cropped to only contain the message bubbles and none of the navigation bar of the text input bar (expect the the first and last screencaps of course) but I don't know how to detect where to line up the images.
I need to detect where there is overlap in the conversations and then stitch the images at the point. (I know how to draw the images to a new image context too.)
I am looking for an open source framework that could help me achieve this and any advice as to how to accomplish this task.
Thanks!
You can also give a go to the following code:
https://github.com/foundry/OpenCVStitch
While it might be overkill for your project, you could have a look at PanoTools: an Open Source software library for manipulating and stitching panoramic images. It's portable (Win/Lin/Mac), and if you're looking forward to making the stitching on your computer, GUIs to it like Hugin may even already fit your use case (I only used them for stitching photographs, so check the projection settings).