diagplot.volcano {metaseqR} | R Documentation |
This function plots a volcano plot or returns a JSON string which is used to render aninteractive in case of HTML reporting.
diagplot.volcano(f, p, con = NULL, fcut = 1, pcut = 0.05, alt.names = NULL, output = "x11", path = NULL, ...)
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 |
output |
one or more R plotting device to direct the
plot result to. Supported mechanisms: |
path |
the path to create output files. |
... |
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.
Panagiotis Moulos
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")