plot.associations: Plot of 'associations' objects

In dynOmics: Fast Fourier Transform to Identify Associations Between Time Course Omics Data

Description

Plot showing the associated trajectories with or without estimated time shift.

Usage

## S3 method for class 'associations'
plot(x, data1, data2, time, feature1, feature2, cutoff,
  fdr = T, absCor = T, withShift = F, ...)

Arguments

x	an object of class associations
data1	an object of class matrix or data.frame.
data2	an object of class matrix or data.frame.
time	a vector of class numeric presenting the measured time points.
feature1	the reference feature to visualise, either the index or the name.
feature2	the associated feature to visualise, either the index or the name.
cutoff	for the associated feature. If fdr=TRUE the false discovery rate (fdr) corrected p-value (default cutoff=0.05). If fdr=FALSE the absolute Pearson Correlation cutoff (default cutoff=0.9).
fdr	(default TRUE) indicating if the false discovery rate of the corrected p-values from the associations object should be used as cutoff to visualize associated profiles. If FALSE the absolute Peason correlation is used as cutoff.
absCor	(default FALSE) if fdr=FALSE you can choose to visualise associations invariant for positive or negative correlation.
withShift	(default FALSE) indicating if the associated feature should be plotted with the time shift.
...	ignored

Details

The function allows to visualise features with and without realignement (or shift) of the time profiles according to the estimated delays using associateData() function from the dynOmics package. Features to be visualised can be filtered either using FDR corrected p-values or a correlation threshold.

Value

plot showing the associated data as calculated by associateData()

See Also

associateData, summary.associations

Examples

## Not run: 
data(Metabolites)
data(Transcripts)
associations <- associateData(Metabolites[,1:2],Transcripts[,c(1:100)])
#if you only define feature1 or feature2 if will plot all associations
plot(associations,Metabolites,Transcripts,feature1=1,withShift = TRUE)
#if you define feature1 and feature2 it will only plot these two profiles
plot(associations,Metabolites,Transcripts,feature1="Metabolite 1",feature2="Transcript 2")

## End(Not run)

dynOmics documentation built on May 1, 2019, 8:42 p.m.