| 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)