GPPlot {tigre} | R Documentation |
Plots GP(DI)SIM models.
GPPlot(data, savepath = '', nameMapping = NULL, predt = NULL, fileOutput=FALSE, plotTime=NULL)
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! |
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).
Antti Honkela
## 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)