plotMA {DESeq2} | R Documentation |
A simple helper function that makes a so-called "MA-plot", i.e. a scatter plot of log2 fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis).
## S4 method for signature 'DESeqResults' plotMA(object, alpha, main, ylim, ...) ## S4 method for signature 'DESeqDataSet' plotMA(object, alpha, main, ylim, ...) ## S4 method for signature 'DESeqDataSet' plotMA(object, alpha = 0.1, main = "", ylim, ...) ## S4 method for signature 'DESeqResults' plotMA(object, alpha = 0.1, main = "", ylim, ...)
object |
a |
alpha |
the significance level for thresholding adjusted p-values |
main |
optional title for the plot |
ylim |
optional y limits |
... |
further arguments passed to |
This function is essentially two lines of code: building a
data.frame
and passing this to the plotMA
method for data.frame
from the geneplotter package.
The code of this function can be seen with:
getMethod("plotMA","DESeqDataSet")
If users wish to
modify the graphical parameters of the plot, it is
recommended to build the data.frame in the same manner and
call plotMA
A trellis
object.
Michael Love
dds <- makeExampleDESeqDataSet() dds <- DESeq(dds) plotMA(dds) res <- results(dds) plotMA(res)