tpptrPlotSplines: Plot spline fits per protein

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description

Plot spline fits per protein

Usage

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
)

Arguments

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)

Details

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).

Value

None

See Also

ns, AICc, tpptrFitSplines, tpptrFTest

Examples

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())

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.