tpptrPlotSplines: Plot spline fits per protein
In TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Details Value See Also Examples

Plot spline fits per protein

tpptrPlotSplines(
  data,
  factorsH1 = NULL,
  factorsH0 = NULL,
  fittedModels,
  testResults,
  resultPath = NULL,
  individual = TRUE,
  overview = FALSE,
  returnPlots = FALSE,
  control = list(nCores = "max", maxRank = 500, highlightBelow = 0.05),
  maxRank = NULL,
  highlightBelow = NULL,
  plotIndividual = NULL,
  plotAlphabetical = NULL
)

`data`	long table of proteins measurements that were used for spline fitting.
`factorsH1`	DEPRECATED
`factorsH0`	DEPRECATED
`fittedModels`	long table of fitted models. Output of `tpptrFitSplines`.
`testResults`	long table of p-values per protein. Output of `tpptrFTest`.
`resultPath`	an optional character vector with the name of the path where the plots should be saved.
`individual`	logical. Export each plot to individual files?
`overview`	logical. Generate summary pdfs?
`returnPlots`	logical. Should the ggplot objects be returned as well?
`control`	a list of general settings.
`maxRank`	DEPRECATED
`highlightBelow`	DEPRECATED
`plotIndividual`	DEPRECATED
`plotAlphabetical`	DEPRECATED Contains the following fields: `nCores`: number of CPUs for parallel production of plots per protein if `individual = TRUE` (default: "max") `maxRank`: how many of the top hits should be plotted if `overview = TRUE` (default: 500) `highlightBelow`: maximum adjusted p-value for which a protein is highlighted by a different background color if `overview = TRUE` (default: 0.05)

Plots of the natural spline fits will be stored in a subfolder with name Spline_Fits at the location specified by resultPath.

Exporting each plot to individual files (individual = TRUE) can cost runtime and the resulting files can be tedious to browse. If you just want to browse the results, use overview = TRUE instead.

If overview = TRUE, two summary PDFs are created that enable quick browsing through all results. They contain the plots in alphacetical order (splineFit_alphabetical.pdf), or ranked by p-values (splineFit_top_xx.pdf, where xx is the maximum rank defined by overviewSettings$maxRank).

None

ns, AICc, tpptrFitSplines, tpptrFTest

data(hdacTR_smallExample)
tpptrData <- tpptrImport(configTable = hdacTR_config, data = hdacTR_data)
tidyData <- tpptrTidyUpESets(tpptrData)
splineFits <- tpptrFitSplines(data = tidyData, nCores = 1, splineDF = 4:5,
                              factorsH1 = "condition", returnModels = TRUE)
testResults <- tpptrFTest(fittedModels = splineFits, doPlot = FALSE)
tpptrPlotSplines(data = tidyData, fittedModels = splineFits,
                 individual = FALSE,
                 testResults = testResults, resultPath = getwd())