diagplot.boxplot {metaseqR} | R Documentation |
A wrapper over the general boxplot function, suitable for matrices produced and processed with the metaseqr package. Intended for internal use but can be easily used as stand-alone. It can colors boxes based on group depending on the name argument.
diagplot.boxplot(mat, name = NULL, log.it = "auto", y.lim = "default", is.norm = FALSE, output = "x11", path = NULL, alt.names = NULL, ...)
mat |
the count data matrix. |
name |
the names of the samples plotted on the
boxdiagplot. If |
log.it |
whether to log transform the values of mat
or not. It can be |
y.lim |
custom y-axis limits. Leave the string
|
is.norm |
a logical indicating whether object contains raw or normalized data. It is not essential and it serves only plot annotation purposes. |
output |
one or more R plotting device to direct the
plot result to. Supported mechanisms: |
path |
the path to create output files. |
alt.names |
an optional vector of names, e.g. HUGO
gene symbols, alternative or complementary to the unique
rownames of |
... |
further arguments to be passed to plot
devices, such as parameter from |
The filename of the boxplot produced if it's a file.
Panagiotis Moulos
# Non-normalized boxplot require(DESeq) data.matrix <- counts(makeExampleCountDataSet()) sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3")) diagplot.boxplot(data.matrix,sample.list) # Normalized boxplot norm.args <- get.defaults("normalization","deseq") object <- normalize.deseq(data.matrix,sample.list,norm.args) diagplot.boxplot(object,sample.list)