LOB_viewdata: Vizualize lipids annotated by LOBSTAHS with live graphs in...
In hholm/LOB_tools: Additional Data Screening And Cleaning Tools For LOBSTAHS
LOB_viewdata R Documentation
Vizualize lipids annotated by LOBSTAHS with live graphs in shiny
Description
This function launches a shiny app to graph detected lipids in retention time verse m/z space. Graphs can be colored based on multipul screening criteria in order visualize data and identify correct or suspect annoations.
Usage
LOB_viewdata(peakdata, rawSpec = NULL)
Arguments
peakdata
A object of class LOBSet or data.frame generated with getLOBpeaklist() that contains the peakdata of identifed lipids.
rawSpec
If the user chooses, a XCMSnExp object to be searched contianing both MS1 and MS2 spectra that the peakdata was generated from. LOB_findMS2() can be run within the shiny app to detect MS2 spectra that may correspond with annotated peaks.
Details
Runs a shiny app that allows for multipul visualizations of the LOBSTAHS generated lipid annotations. Annotations can be viewed by class, double bonds, carbon number, oxidation, retantion time, screening criteria, and more. In addition to this, the GUI allows for easy passing of mz and rt info to LOB_findMS2(). Peaks may be selected by clicking to display their metadata and multipul annotations in a table. MS2 spectra of annotated peaks may be identifed elsewhere using the the output of LOB_findMS2() which is displayed in app.
Value
A shiny app.
Note
Currently in development.
Author(s)
Henry Holm, hholm@mit.edu
Dan Lowenstien, dlowenstein@whoi.edu
Max Jahns, mjahns@mit.edu
Shavonna Bent, sbent@mit.edu
Examples
# View PtH2O2lipids annotation LOBSet
LOBSet <- PtH2O2lipids::ptH2O2lipids$LOBSet
LOB_viewdata(LOBSet)
hholm/LOB_tools documentation built on Jan. 28, 2024, 12:08 p.m.
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| LOB_viewdata | R Documentation |
Vizualize lipids annotated by LOBSTAHS with live graphs in shiny
Description
This function launches a shiny app to graph detected lipids in retention time verse m/z space. Graphs can be colored based on multipul screening criteria in order visualize data and identify correct or suspect annoations.
Usage
LOB_viewdata(peakdata, rawSpec = NULL)
Arguments
peakdata |
A object of class |
rawSpec |
If the user chooses, a |
Details
Runs a shiny app that allows for multipul visualizations of the LOBSTAHS generated lipid annotations. Annotations can be viewed by class, double bonds, carbon number, oxidation, retantion time, screening criteria, and more. In addition to this, the GUI allows for easy passing of mz and rt info to LOB_findMS2(). Peaks may be selected by clicking to display their metadata and multipul annotations in a table. MS2 spectra of annotated peaks may be identifed elsewhere using the the output of LOB_findMS2() which is displayed in app.
Value
A shiny app.
Note
Currently in development.
Author(s)
Henry Holm, hholm@mit.edu
Dan Lowenstien, dlowenstein@whoi.edu
Max Jahns, mjahns@mit.edu
Shavonna Bent, sbent@mit.edu
Examples
# View PtH2O2lipids annotation LOBSet
LOBSet <- PtH2O2lipids::ptH2O2lipids$LOBSet
LOB_viewdata(LOBSet)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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