tpptrPlotSplines {TPP} | R Documentation |
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 |
testResults |
long table of p-values per protein.
Output of |
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:
|
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())