diagplotBoxplot {metaseqR2} | 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.
diagplotBoxplot(mat, name = NULL, logIt = "auto", yLim = "default", isNorm = FALSE, output = "x11", path = NULL, altNames = NULL, ...)
mat |
the count data matrix. |
name |
the names of the samples plotted on the boxplot. See also Details. |
logIt |
whether to log transform the values of mat
or not. It can be |
yLim |
custom y-axis limits. Leave the string
|
isNorm |
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. |
altNames |
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 |
Regarding name
, if NULL
, the function check
the column names of mat
. If they are also
NULL
, sample names are autogenerated. If
name="none"
, no sample names are plotted. If name
is a list, it should be the sampleList argument provided
to the manin metaseqr2 function. In that case, the boxes
are colored per group.
The filename of the boxplot produced if it's a file.
Panagiotis Moulos
# Non-normalized boxplot require(DESeq2) dataMatrix <- metaseqR2:::exampleCountData(2000) sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3")) diagplotBoxplot(dataMatrix,sampleList) # Normalized boxplot normArgs <- getDefaults("normalization","deseq2") object <- normalizeDeseq2(dataMatrix,sampleList,normArgs) diagplotBoxplot(object,sampleList)