tpp2dSplinePlot {TPP} | R Documentation

## Fit splines and generate ggplot visualizations

### Description

Fit splines through TR reference dataset and extrapolates relative 2D-TPP datapoints, then compares spline fits of different treatments with non-treatment with an f-test

### Usage

    tpp2dSplinePlot(data_2D = NULL, trRef = NULL, fcStr = NULL,
      idVar = NULL, refIdVar = "Protein_ID", methods = c("doseResponse",
      "splineFit"), refFcStr = "norm_rel_fc_protein_", verbose = FALSE)

### Arguments

`data_2D` | result data.frame from a 2D-TPP CCR analysis
`trRef` | character string of a valid system path to a TPP-TR reference RData object
`fcStr` | character string indicating how columns that will contain the actual fold change values will be called. The suffix `fcStr` will be pasted in front of the names of the experiments.
`idVar` | character string indicating name of the columns containing the unique protein identifiers in the 2D data set
`refIdVar` | character string indicating name of the columns containing the unique protein identifiers in the reference data set
`methods` | vector of character strings that indicate which methods has been used for the previous analysis (default: c("doseResponse"), alternative: c("splineFit") or c("doseResponse", "splineFit"))
`refFcStr` | character string indicating how columns that will contain the fold change values in the reference data set
`verbose` | print description of problems for each protein for which splines fits could not be performed

### Value

A list of ggplots which can be accessed via the unique protein ids in the idVar column

### Examples

    load(system.file("example_data/2D_example_data/shortData2d.RData", package="TPP"))
    trRef <- system.file("example_data/2D_example_data/referenceNormData.RData", package="TPP")

[Package TPP version 3.10.1 Index]