tpp2dCreateDRplots {TPP} | R Documentation

## Create dose response curve plots for 2D-TPP data

### Description

Generates a list of dose response curve plots per protein and temperature point.

### Usage

    tpp2dCreateDRplots(
      data = NULL,
      type = "all",
      verbose = FALSE,
      paletteName = "Spectral"
    )

### Arguments

`data` | the data that should be plotted.
`type` | string defining which curves to display (see details).
`verbose` | boolean variable stating whether a print description of problems/success for plotting of each protein should be printed.
`paletteName` | color palette (see details).

### Details

`data` is a data frame in wide table format returned by function `tpp2dCurveFit`. Its attributes contain information about the experiment names, temperatures, isobaric labels, as well as instructions on how to find the relevant columns in the wide table.

`type` defines which curves to display per plot. Possible values are:

- "all": Create one plot per protein. This plot simultaneously displays the curves for all available temperatures for this protein (the default).

- "good": Create one plot per protein. This plot displays all dose response curves with a high goodness-of-fit. Choose this option to save runtime by focusing only on the reliable fits.

- "single": Create one separate plot per protein and temperature. This plot displays all dose response curves with a high goodness-of-fit.

`paletteName` specifies the color palette to be used by the `brewer.pal` function from the `RColorBrewer` package to assign a separate color to each concentration.

### Value

A list of successfully generated plot objects of class `'ggplot'`

### See Also

`tpp2dCurveFit` `brewer.pal`

### Examples

    data(panobinostat_2DTPP_smallExample)

    # Import data:
    datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config,
                          data = panobinostat_2DTPP_data,
                          idVar = "representative",
                          addCol = "clustername",
                          intensityStr = "sumionarea_protein_",
                          nonZeroCols = "qusm")

    # Compute fold changes:
    fcData2d <- tpp2dComputeFoldChanges(data = datIn)
    normData2d <- tpp2dNormalize(data = fcData2d)
    ccr2dResults <- tpp2dCurveFit(data = normData2d)
    allCurves <- tpp2dCreateDRplots(data = ccr2dResults, type = "all")
    allCurves[["HDAC1"]]

[Package TPP version 3.16.5 Index]