Unable to lock color map intensity scale for ion images in PythonAPI

[RRKV]

Hi
In the METASPACE webapp I am able to lock the color scale for the ion images to a certain intensity (picture attached) which helps in visually comparing response between different m/z values. I'd like to be able to do this as well when working with ion images in the PythonAPI, but after reading through the documentation and experimenting on my own I haven't found a way to do this. Is this something that is currently implemented or can you advise on how to accomplish this? Thank you!

[Bisho2122]

Hi @RRKV, thank you for your question. May I ask how do you usually use the API to visualize the ion images. Are you using the IsotopeImages.plot() method ?.

If you can provide an example for how do you usually visualize it with API, I can provide a simple snippet or a script to have lower/upper boundries on the intensity scale for a set of ion images.

[RRKV]

Hi @Bisho2122, thank you for the quick response. I have not been using the IsotopeImages.plot() method, but instead using matplotlib with the values from the dataset.isotope_images() method. The attached photo is an example from the documentation that I have followed to generate my images. Thanks for your help!

[Bisho2122]

Great, so in the example that you provided. You can access the intensity array for the 4 isotope images through images._images. The output of this is a list of 4 arrays where each array is ion image of one isotopic peak. Once you have the list of arrays, you can run a custom function that can clip each array by a specified lower or upper boundary which should equivalent to locking the intensities in the web version.

For reference check the this class here which is the class of images object in your code.

We'll try to add a clipping method to this class in the future so you won't have to write a custom function for it.

Hope that helps

[RRKV]

Thank you again for your response. I think I understand what you're saying, but I don't think that solves the issue. Clipping the values just change the data that is going in, which would help if I was just trying to prevent values smaller than or larger than the minimum or maximum desired value, respectively, but this doesn't lock the color scale for the set of images when all values are within the clip boundaries.

As I was making an example, I realized that just setting the color scale measurements as vmin and vmax in the plt.imshow call accomplishes the functionality I am looking for. I've included the example image for clarity. The desired output was the "Color Scale Lock" column where regardless of the max or min value per image the same value corresponds to the same color across images (see 6 in each image in column 3). This isn't accomplished by clipping values (using np.clip) since across images different values correspond to the same color (see 10, 9, and 7 in the three images in column 2).

Thank you again for your help and advice, I appreciate it!

[Bisho2122]

You're absolutely right. It's just adjusting the color scale in plt.imshow. I also thought about it earlier and was a bit confused about why one would want to change or clip the image arrays if the purpose was purely visualization and I overthought it :D. Happens sometimes :).

Glad that the problem is solved. And if there's anything else that you'd like to be added or implemented in the API. You can share your ideas here