diagplot.de.heatmap {metaseqR} | R Documentation |
This function plots a heatmap of the differentially expressed genes produced by the metaseqr workflow, useful for quality control, e.g. whether samples belonging to the same group cluster together.
diagplot.de.heatmap(x, con = NULL, output = "x11", path = NULL, ...)
x |
the data matrix to create a heatmap for. |
con |
an optional string depicting a name (e.g. the contrast name) to appear in the title of the volcano plot. |
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) diagplot.de.heatmap(data.matrix[p[[1]]<0.05,])