metaseqR (version 1.12.2)

diagplot.volcano: (Interactive) volcano plots of differentially expressed genes

Description

This function plots a volcano plot or returns a JSON string which is used to render aninteractive in case of HTML reporting.

Usage

diagplot.volcano(f, p, con = NULL, fcut = 1, pcut = 0.05,
        alt.names = NULL, output = "x11", path = NULL, ...)

Arguments

f

the fold changes which are to be plotted on the x-axis.

p

the p-values whose -log10 transformation is going to be plotted on the y-axis.

con

an optional string depicting a name (e.g. the contrast name) to appear in the title of the volcano diagplot.

fcut

a fold change cutoff so as to draw two vertical lines indicating the cutoff threshold for biological significance.

pcut

a p-value cutoff so as to draw a horizontal line indicating the cutoff threshold for statistical significance.

alt.names

an optional vector of names, e.g. HUGO gene symbols, alternative or complementary to the unique names of f or p (one of them must be named!). It is used only in JSON output.

output

one or more R plotting device to direct the plot result to. Supported mechanisms: "x11" (default), "png", "jpg", "bmp", "pdf", "ps" or "json". The latter is currently available for the creation of interactive volcano plots only when reporting the output, through the highcharts javascript library.

path

the path to create output files.

...

further arguments to be passed to plot devices, such as parameter from par.

Value

• The filenames of the plots produced in a named list with names the which.plot argument. If output="x11", no output filenames are produced.

Examples

require(DESeq)
data.matrix <- counts(makeExampleCountDataSet())
sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
contrast <- "A_vs_B"
M <- normalize.edger(data.matrix,sample.list)
p <- stat.edger(M,sample.list,contrast)
ma <- apply(M[,sample.list$A],1,mean)
mb <- apply(M[,sample.list$B],1,mean)
f <- log2(ifelse(mb==0,1,mb)/ifelse(ma==0,1,ma))
diagplot.volcano(f,p[[1]],con=contrast)
#j <- diagplot.volcano(f,p[[1]],con=contrast,output="json")