tpp2dCreateDRplots: Create dose response curve plots for 2D-TPP data

Description Usage Arguments Details Value See Also Examples

View source: R/tpp2dCreateDRplots.R

Description

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

Usage

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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:

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

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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"]]

TPP documentation built on Nov. 8, 2020, 5:55 p.m.