Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Python bindings don't work correctly in latest version of RStudio without altering Python settings (ModuleNotFoundError) #13

Open
ethanbass opened this issue Feb 4, 2023 · 14 comments
Open

Python bindings don't work correctly in latest version of RStudio without altering Python settings (ModuleNotFoundError) #13

ethanbass opened this issue Feb 4, 2023 · 14 comments
Labels
wontfix This will not be worked on

Comments

@ethanbass
Copy link
Owner

Recent versions of RStudio made some strange changes to the way reticulate functions, as discussed in this thread, which interfere with chromConverter's python bindings. chromConverter will still load but python-based parsers will likely not be available if a project is loaded. When trying to access python parsers, a module not found error will be generated. As far as I can tell, this is a bug with RStudio rather than chromConverter (though RStudio developers seem to think this is the expected behavior).

This issue can apparently be resolved by unchecking a box in the RStudio settings. To do this, open RStudio settings and navigate to the Python pane (Tools:Global Options:Python). Then uncheck the box that says "Automatically activate project-local Python environments" and click Apply. RStudio must then be restarted for the settings to take effect.
@ethanbass ethanbass changed the title Python bindings don't work correctly in latest version of RStudio without altering Python settings Python bindings don't work correctly in latest version of RStudio without altering Python settings (ModuleNotFoundError) Feb 5, 2023
@ethanbass ethanbass added the wontfix This will not be worked on label Feb 8, 2023
@nathan-loves-soil
Copy link

Hi Ethan, I'm trying to use the rainbow parser in RStudio for Chemstation data file with an ".MS" extension.

dat <- chromConverter::read_chroms(path_to_files, format_in = "chemstation", parser = "rainbow")

Still after unchecking the box in the above post, I'm getting the following error:

Warning in chromConverter::read_chroms(path_to_files, format_in = "chemstation", :
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'rainbow'
Run reticulate::py_last_error() for details.
The following chromatograms could not be interpreted: 1

I'm pretty sure I've got the right package for Python installed (rainbow-api), and I've told reticulate to use the latest version of Python.
Any thoughts where I might be going wrong?

(also sorry if this isn't the correct place to ask this question, feel free to move this query somewhere else)
Thank you,

Nathan

@ethanbass
Copy link
Owner Author

Hi Nathan,
Do you have miniconda installed? Could you try running, chromConverter::configure_python_environment("rainbow") and then post the output here?
Ethan

@nathan-loves-soil
Copy link

Hi Ethan,

No I didn't have miniconda installed, but I do now. I ran the line that you provided, and it gave me the option to install it then, so I did. Output was very long, so I won't post it here.
I restarted the R session and then tried running my code again, but got the same error as before.

I just ran your line again, here is the ouput:

chromConverter::configure_python_environment("rainbow")

C:\Users\20373478\OneDrive - Curtin\All R Projects\py-GC-MS Library Searches\py_GC_MS_reports>CALL "C:\Users\20373478\AppData\Local\r-miniconda\condabin\activate.bat" "chromConverter"

C:\Users\20373478\OneDrive - Curtin\All R Projects\py-GC-MS Library Searches\py_GC_MS_reports>conda.bat activate "chromConverter"
Requirement already satisfied: rainbow-api in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (1.0.9)
Requirement already satisfied: numpy in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from rainbow-api) (2.0.0)
Requirement already satisfied: matplotlib in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from rainbow-api) (3.9.1)
Requirement already satisfied: lxml in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from rainbow-api) (5.2.2)
Requirement already satisfied: pandas in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from rainbow-api) (2.2.2)
Requirement already satisfied: contourpy>=1.0.1 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (1.2.1)
Requirement already satisfied: cycler>=0.10 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (4.53.1)
Requirement already satisfied: kiwisolver>=1.3.1 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (1.4.5)
Requirement already satisfied: packaging>=20.0 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (24.1)
Requirement already satisfied: pillow>=8 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (10.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (3.1.2)
Requirement already satisfied: python-dateutil>=2.7 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from matplotlib->rainbow-api) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from pandas->rainbow-api) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from pandas->rainbow-api) (2024.1)
Requirement already satisfied: six>=1.5 in c:\users\20373478\appdata\local\r-miniconda\envs\chromconverter\lib\site-packages (from python-dateutil>=2.7->matplotlib->rainbow-api) (1.16.0)
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'rainbow'
Run reticulate::py_last_error() for details.

Thank you for your assistance :)

@ethanbass
Copy link
Owner Author

This seems to be a reticulate configuration issue, since you have rainbow installed in the chromConverter environment, but reticulate isn't finding it. I'm not sure exactly what the issue might be though. Did you restart your R session after installing miniconda and all that? It could be that reticulate has already loaded a different python environment in your R session and can't switch to the chromConverter environment.

@nathan-loves-soil
Copy link

Oh yep okay. Thanks, that is sorted now, I realised I had a line instructing what version of python to use [ reticulate::use_python() ] , so I've commented that out and the script runs.
However, there's a new error, seems like it's having an issue parsing the file maybe?

path_to_files <- "C:\\gcms\\1\\data\\py_GC_MS\\B121468.D\\DATA.MS"  
dat <- chromConverter::read_chroms(path_to_files, format_in = "chemstation", parser = "rainbow")

C:\Users\20373478\OneDrive - Curtin\All R Projects\py-GC-MS Library Searches\py_GC_MS_reports>CALL "C:\Users\20373478\AppData\Local\r-miniconda\condabin\activate.bat" "C:\Users\20373478\AppData\Local\r-miniconda\envs\r-reticulate"

C:\Users\20373478\OneDrive - Curtin\All R Projects\py-GC-MS Library Searches\py_GC_MS_reports>conda.bat activate "C:\Users\20373478\AppData\Local\r-miniconda\envs\r-reticulate"
Requirement already satisfied: aston in c:\users\20373478\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (0.7.1)
Requirement already satisfied: numpy in c:\users\20373478\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (2.0.0)
Requirement already satisfied: scipy>=1.2.0 in c:\users\20373478\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from aston) (1.14.0)
Done!
Warning in chromConverter::read_chroms(path_to_files, format_in = "chemstation", :
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
ValueError: strides is incompatible with shape of requested array and size of buffer
Run reticulate::py_last_error() for details.

The following chromatograms could not be interpreted: 1

Thanks again!!

@ethanbass
Copy link
Owner Author

ethanbass commented Jul 10, 2024 •
edited
Loading

Ah, i see. That would do it. Can you send a copy of the file? Could be a format that isn't yet supported by rainbow? (There are multiple .MS formats produced by different versions of chemstation and openlab). Also do you happen to know what version of chemstation the file came from?

@nathan-loves-soil
Copy link

GitHub doesn't like the .MS file type being attached in a comment. What would be your preferred way for me to send it to you?

Unfortunately I don't know what version of the software it has come from. I suspect it's pretty old as the GC-MS that we used is fairly old. If it's important to know, I can find out next week what version the computer attached to the GC-MS uses.
The version that I have on my PC which can read the file is MSD ChemStation F.01.03.2357.

Thank you Ethan!

@ethanbass
Copy link
Owner Author

ethanbass commented Jul 12, 2024 via email

@ethanbass
Copy link
Owner Author

ethanbass commented Jul 15, 2024 •
edited
Loading

Hi Nathan,
I just found your file in my spam folder. I am also getting the same error message with rainbow, but the entab parser seems to be able to read your file (see installation instructions here: https://github.com/ethanbass/chromConverter/?tab=readme-ov-file#entab). Would this be an option for you? I will also try to look into where rainbow is running into problems, but I'm not sure when I'll get around to it. You could also post an issue on the rainbow github page (https://github.com/evanyeyeye/rainbow/) if you like. It's possible they might get to it sooner.

Ethan

@nathan-loves-soil
Copy link

Hi Ethan, I will give that a go this week! I'll let you know how I go with using the entab parser.
Thanks so much for your help

@nathan-loves-soil
Copy link

Hey Ethan, just letting you know that the entab parser worked for me! I really appreciated your willingness to help with troubleshooting this with me. Thanks again, Nathan

@ethanbass
Copy link
Owner Author

ethanbass commented Jul 16, 2024 via email

@nathan-loves-soil
Copy link

nathan-loves-soil commented Aug 16, 2024 via email

@ethanbass
Copy link
Owner Author

ethanbass commented Aug 16, 2024 •
edited
Loading

Hi Nathan,

The intensity should be the intensity at each mass fragment as specified by the mz column. You would calculate the TIC by summing over all the mz values at each time point, e.g.:

library(dplyr)
x<-dat[[1]]
tic <- x |> group_by(rt) |> summarize_at("intensity",sum) 
matplot(tic$rt, tic$intensity,type='l')

You should be able to extract the mass spectrum for whichever retention time by filtering on time, e.g., to get the mass spectrum of the first scan, you could do:

times <- unique(x$rt)
spec <- x[x$rt == times[1], -1]

Here is a simple plot function you could use to plot the mass spectrum in base R:

plot_spec <- function(spec, lab_int=0.2, digits=1){
  plot(spec, type = "h")
  lab.idx <- which(spec$intensity > lab_int * max(spec$intensity))
  text(spec$mz[lab.idx], spec$intensity[lab.idx], round(spec$mz[lab.idx], 
                    digits), offset = 0.25, pos = 3, cex = 0.5)
}

So you should be able to do :
plot_spec(spec).

Hopefully that helps?

Ethan

Also, I'm not sure what you were thinking of doing for database search? I have some functions in my mzinspectr package (https://github.com/ethanbass/mzinspectr/) that you could check out, but it's still pretty poorly documented still and isn't really oriented toward analyzing raw GC-MS data at least in the current iteration.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
wontfix This will not be worked on
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ethanbass @nathan-loves-soil