Description Usage Arguments Value Author(s) Examples
Creates a Multi-Dimensional Scale plot for the given samples based on the count data matrix. MDS plots are very useful for quality control as you can easily see of samples of the same groups are clustered together based on the whole dataset.
1 2 | diagplotMds(x, sampleList, method = "spearman",
logIt = TRUE, output = "x11", path = NULL, ...)
|
x |
the count data matrix. |
sampleList |
the list containing condition names and the samples under each condition. |
method |
which correlation method to use. Same as
the method parameter in |
logIt |
whether to log transform the values of x or not. |
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 filename of the MDS plot produced if it's a file.
Panagiotis Moulos
1 2 3 | dataMatrix <- metaseqR2:::exampleCountData(5000)
sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
diagplotMds(dataMatrix,sampleList)
|
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