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protViz / deisotoper

Implementation, development, and evaluation of algorithms for the detection and extraction of isotope pattern of a mass spectrometric measurement.

https://CRAN.R-project.org/package=deisotoper

GNU General Public License v3.0

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Shiny #28

Open LucasSchmidt97 opened 7 years ago

LucasSchmidt97 commented 7 years ago

tutorials shiny https://shiny.rstudio.com/tutorial/
- hello world shiny app
dat files to rdata (bfabric) https://fgcz-bfabric.uzh.ch/bfabric/userlab/show-application.html?applicationId=155&tab=details
2 mascot dat files (rdata) input

LucasSchmidt97 commented 7 years ago

build a diff function which shows where the spectra differ and mark it in the plot

LucasSchmidt97 commented 7 years ago

sorted mascot score

R> idx.score <- order(as.numeric(protViz:::.get_q_peptide(F225712,
attribute = 'pep_score')), decreasing = TRUE)
R> plot(pep_score[idx.score])

color (green and dark green)
xlim (0, 2000)
slider for zooming on the x-axis

LucasSchmidt97 commented 7 years ago

spectrum index (+10/-10)
y Scala same (DOESN'T WORK because bug in ProtViz)
scaling of display for all resolutions
ions diff like mz diff
x scale with values
peptide sequence (behind mascot score)

LucasSchmidt97 commented 7 years ago

add more info about the Spectra (query number, etc)

LucasSchmidt97 commented 7 years ago

slider/config for itol and other parameters in peakplot

LucasSchmidt97 commented 7 years ago

show Delta masses between peaks to see differences

LucasSchmidt97 commented 7 years ago

Fix checkboxgroup bug

LucasSchmidt97 commented 7 years ago

Shiny app runs and is useful/works, but some bugs occur because of the data differences.

LucasSchmidt97 commented 7 years ago

Update shiny app because of new R interface