Description Usage Arguments Details Value Author(s) Examples
Methods for objects of classes
matrix
,
ExpressionSet
,
vsn
and
MAList
to plot row standard deviations versus row means.
1 2 3 4 5 6 7 8 |
x |
An object of class
|
ranks |
Logical, indicating whether the x-axis (means) should be plotted
on the original scale ( |
xlab |
Character, label for the x-axis. |
ylab |
Character, label for the y-axis. |
pch |
Ignored - exists for backward compatibility. |
plot |
Logical. If |
bins |
Gets passed on to |
... |
Further arguments that get passed on to |
Standard deviation and mean are calculated row-wise from the
expression matrix (in) x
. The scatterplot of these versus each other
allows you to visually verify whether there is a dependence of the standard
deviation (or variance) on the mean.
The red line depicts the running median estimator (window-width 10%).
If there is no variance-mean dependence, then the line should be approximately horizontal.
A named list with five components: its elements px
and
py
are the x- and y-coordinates of the individual data points
in the plot; its first and second element are the x-coordinates and values of
the running median estimator (the red line in the plot).
Its element gg
is the plot object (see examples).
Depending on the value of plot
, the method can (and by default does) have a side effect,
which is to print gg
on the active graphics device.
Wolfgang Huber
1 2 3 4 5 6 7 8 9 10 11 | data("kidney")
log.na <- function(x) log(ifelse(x>0, x, NA))
exprs(kidney) <- log.na(exprs(kidney))
msd <- meanSdPlot(kidney)
## The `ggplot` object is returned in list element `gg`, here is an example of how to modify the plot
library("ggplot2")
msd$gg + ggtitle("Hello world") + scale_fill_gradient(low = "yellow", high = "darkred") + scale_y_continuous(limits = c(0, 7))
## Try this out with not log-transformed data, vsn2-transformed data, the lymphoma data, your data ...
|
Loading required package: Biobase
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Attaching package: 'BiocGenerics'
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clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
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pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
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