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 'DESeqDataSet' plotMA(object, alpha = 0.1, main = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...) ## S4 method for signature 'DESeqResults' plotMA(object, alpha, main = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...)
object |
a |
alpha |
the significance level for thresholding adjusted p-values |
main |
optional title for the plot |
xlab |
optional defaults to "mean of normalized counts" |
ylim |
optional y limits |
MLE |
if |
... |
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
.
If the object
contains a column svalue
then these
will be used for coloring the points (with a default alpha=0.005
).
Michael Love
dds <- makeExampleDESeqDataSet() dds <- DESeq(dds) plotMA(dds) res <- results(dds) plotMA(res)