Description Usage Arguments Value Author(s) Examples
View source: R/metaseqr.plot.R
This function uses the R package VennDiagram and plots an up to 5way Venn diagram depicting the common and specific to each statistical algorithm genes, for each contrast. Mostly for internal use because of its main argument which is difficult to construct, but can be used independently if the user grasps the logic.
1 2 3 4  diagplot.venn(pmat, fcmat = NULL, pcut = 0.05,
fcut = 0.5, direction = c("dereg", "up", "down"),
nam = as.character(round(1000 * runif(1))),
output = "x11", path = NULL, alt.names = NULL, ...)

pmat 
a matrix with pvalues corresponding to the
application of each statistical algorithm. The pvalue
matrix must have the colnames attribute and the colnames
should correspond to the name of the algorithm used to
fill the specific column (e.g. if

fcmat 
an optional matrix with fold changes
corresponding to the application of each statistical
algorithm. The fold change matrix must have the colnames
attribute and the colnames should correspond to the name
of the algorithm used to fill the specific column (see
the parameter 
pcut 
if 
fcut 
a pvalue cutoff for statistical
significance. Defaults to 
direction 
if 
nam 
a name to be appended to the output graphics
file (if 
output 
one or more R plotting device to direct the
plot result to. Supported mechanisms: 
path 
the path to create output files. If

alt.names 
an optional named vector of names, e.g.
HUGO gene symbols, alternative or complementary to the
unique gene names which are the rownames of 
... 
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
1 2 3 4 5 6 7 
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