GPPlot {tigre} | R Documentation

## Plot GP(DI)SIM models

### Description

Plots GP(DI)SIM models.

### Usage

    GPPlot(data, savepath = '', nameMapping = NULL, predt = NULL,
           fileOutput=FALSE, plotTime=NULL)

### Arguments

`data` | The model to plot as returned by GPLearn.
`savepath` | The location in the file system where the images are saved.
`nameMapping` | The annotation used for mapping the names of the genes for the figures.
`predt` | The set of time points to use in plotting (default: the time interval covering the data).
`fileOutput` | Is the plot being saved to a file? If yes, do not open new interactive devices for each plot.
`plotTime` | The times of observations to use in the plot. Should usually not be changed!

### Details

The function plots the fitted expression level of the transcription factor (if applicable), the inferred activity of the transcription factor, and the fitted expression level of the target(s).

### Author(s)

Antti Honkela

### See Also

`GPLearn`.

### Examples

    ## Not run:
      # Load a mmgmos preprocessed fragment of the Drosophila developmental
      # time series
      data(drosophila_gpsim_fragment)

      # Get the target probe names
      library(annotate)
      aliasMapping <- getAnnMap("ALIAS2PROBE",
                        annotation(drosophila_gpsim_fragment))
      twi <- get('twi', env=aliasMapping)
      fbgnMapping <- getAnnMap("FLYBASE2PROBE",
                       annotation(drosophila_gpsim_fragment))
      targetProbe <- get('FBgn0035257', env=fbgnMapping)

      # Learn the model
      model <- GPLearn(drosophila_gpsim_fragment,
                       TF=twi, targets=targetProbe,
                       useGpdisim=TRUE, quiet=TRUE)

      # Plot it
      GPPlot(model, nameMapping=getAnnMap("FLYBASE",
             annotation(drosophila_gpsim_fragment)))

    ## End(Not run)

[Package tigre version 1.38.0 Index]