tppccrPlotCurves {TPP} | R Documentation

## Plot dose response curves

### Description

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

### Usage

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

### Arguments

`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.

### Details

`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`.

### Value

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.

### See Also

`tppccrCurveFit`,`tppDefaultTheme`

### Examples

    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)

[Package TPP version 3.20.1 Index]