Comparing two Spectrum1 plots

[Mclnol16]

Hello all,

1. Is there anyway to add/implement a way to compare two Spectrum1 plots?
2. Additionally, is there a way to add a label to a peak other than using base R functions?

Thanks,

Nolan

[lgatto]

See here for spectra comparions.

There is not automated way to annotate peaks in spectra plots at the moment. If you provide some example of what you want to do, we might be able to help.

[Mclnol16]

Thank you for your response,

However, is there a way to plot two Spectrum1 objects against eachother using the plot function? I believe that the plot function will only allow for the comparison of two Spectrum2 objects to be plotted against eachother.

[lgatto]

Indeed. I will see if this couldn't be adapted to work for MS1 data. I don't see any reason it shouldn't.

[lgatto]

It should now work with version 2.11.4 available on Github:

BiocManager::install("lgatto/MSnbase")

[Mclnol16]

@lgatto I am unable to install version 2.11.4 from Github. I have tried reinstalling packages/R/Rstudio and no luck. The error appears to be coming from "mzR"
Here is the final few lines from R :
Error: package or namespace load failed for 'mzR':
(converted from warning) multiple methods tables found for 'analyzer'
Error: package 'mzR' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'MSnbase'

• removing 'C:/Users/nolik/Documents/R/win-library/3.6/MSnbase'
  Error: Failed to install 'MSnbase' from GitHub: (converted from warning) installation of package ‘C:/Users/nolik/AppData/Local/Temp/RtmpG0EbDb/file7587667d35/MSnbase_2.11.4.tar.gz’ had non-zero exit status

Any advice would be appreciated

[lgatto]

Yes, you would need to install the development version of Bioconductor to get the new versions of all the dependencies.

BiocManager::install("MSnbase", version = "devel")

Then try again.

I hope you won't need a more recent version of R for that. Rstudio won't need an update.

[Mclnol16]

Thank you so much! This is perfect!