Description Usage Arguments Value Note Author(s) Examples
View source: R/metaseqr.plot.R
A wrapper around the plotting functions availale in the
NOISeq Bioconductor package. For analytical explanation
of each plot please see the vignette of the NOISeq
package. It is best to use this function through the
main plotting function diagplot.metaseqr
.
1 2 3 4 5 6 
x 
the count data matrix. 
sample.list 
the list containing condition names and the samples under each condition. 
covars 
a list (whose annotation elements are
ideally a subset of an annotation data frame produced by

which.plot 
the NOISeq package plot to generate. It
can be one or more of 
biodist.opts 
a list with the following members: p
(a vector of pvalues, e.g. the pvalues of a contrast),
pcut (a unique number depicting a pvalue cutoff,
required for the 
output 
one or more R plotting device to direct the
plot result to. Supported mechanisms: 
path 
the path to create output files. 
is.norm 
a logical indicating whether object contains raw or normalized data. It is not essential and it serves only plot annotation purposes. 
... 
further arguments to be passed to plot
devices, such as parameter from 
The filenames of the plots produced in a named list with
names the which.plot
argument. If
output="x11"
, no output filenames are produced.
Please note that in case of "biodist"
plots, the
behavior of the function is unstable, mostly due to the
very specific inputs this plotting function accepts in
the NOISeq package. We have tried to predict unstable
behavior and avoid exceptions through the use of tryCatch
but it's still possible that you might run onto an error.
Panagiotis Moulos
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23  require(DESeq)
data.matrix < counts(makeExampleCountDataSet())
sample.list < list(A=c("A1","A2"),B=c("B1","B2","B3"))
lengths < round(1000*runif(nrow(data.matrix)))
starts < round(1000*runif(nrow(data.matrix)))
ends < starts + lengths
covars < list(
data=data.matrix,
length=lengths,
gc=runif(nrow(data.matrix)),
chromosome=data.frame(
chromosome=c(rep("chr1",nrow(data.matrix)/2),
rep("chr2",nrow(data.matrix)/2)),
start=starts,
end=ends
),
factors=data.frame(class=as.class.vector(sample.list)),
biotype=c(rep("protein_coding",nrow(data.matrix)/2),rep("ncRNA",
nrow(data.matrix)/2))
)
p < runif(nrow(data.matrix))
diagplot.noiseq(data.matrix,sample.list,covars=covars,
biodist.opts=list(p=p,pcut=0.1,name="A_vs_B"))

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