tppccrPlotCurves: Plot dose response curves
In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Details Value See Also Examples

tppccrPlotCurves plots the logistic dose response curves, as well as the underlying fold change measurements for each TPP-CCR experiment in a study.

tppccrPlotCurves(
  data = NULL,
  fcTable = NULL,
  curvePars = NULL,
  resultPath = NULL,
  ggplotTheme = tppDefaultTheme(),
  nCores = "max",
  verbose = FALSE
)

`data`	list of expressionSet objects containing protein fold changes, as well as fitted curve parameters.
`fcTable`	optional long table with fold changes for each experiment. Can be provided instead of the input argument `data`.
`curvePars`	optional long table of curve parameters per protein and experiment. Can be provided instead of the input argument `data`.
`resultPath`	location where to store dose-response curve plots.
`ggplotTheme`	ggplot theme for dose response curve plots.
`nCores`	either a numerical value given the desired number of CPUs, or 'max' to automatically assign the maximum possible number (default).
`verbose`	print name of each plotted protein to the command line as a means of progress report.

data is a list of expressionSet objects created by tppccrCurveFit. It contains the isobaric labels and administered drug concentrations in the phenoData and user-defined protein properties (including dose response curve parameters) in the featureData. Protein IDs are stored in the featureNames.

Measurements and compound effects for curve fitting can be provided by the arguments fcTable and cpdEffects, instead of being stored in expressionSets in data.

If specified, fcTable needs to be a long table with column names "id" (the protein names), "concentration" (the fold changes), "labelName" (the isobaric label to each measurement), and "experiment" (e.g. "Vehicle_1" or "Panobinostat_1").

If specified, curvePars needs to be a long table with column names "id" (the protein names), "param" (curve parameter per protein and experiment, see TPP:::drCurveParamNames(names=TRUE, info=FALSE) for possibilities), and "experiment" (e.g. "Vehicle_1" or "Panobinostat_1").

The dose response curve plots will be stored in a subfolder with name DoseResponse_Curves at the location specified by resultPath.

A list of expressionSet objects storing fold changes, as well as row and column metadata. In each expressionSet S, the fold changes can be accessed by Biobase::exprs(S). Protein expNames can be accessed by featureNames(S). Isobaric labels and the corresponding concentrations are returned by S$label and S$concentration. Paths to the produced plots are stored in codefeatureData(S)$plot.

tppccrCurveFit,tppDefaultTheme

data(hdacCCR_smallExample)
tppccrData <- tppccrImport(configTable=hdacCCR_config, 
                           data=hdacCCR_data)
tppccrNorm <- tppccrNormalize(data=tppccrData)
tppccrTransformed <- tppccrTransform(data=tppccrNorm)
tppccrFitted <- tppccrCurveFit(data=tppccrTransformed, nCores=1)
hdacSubset <- sapply(tppccrFitted, function(d)d[grepl("HDAC", rownames(d)),])
tppccrPlotted <- tppccrPlotCurves(hdacSubset, resultPath=getwd(), nCores = 1)