Plot Biological Coefficient of Variation
Plot the genewise biological coefficient of variation (BCV) against gene abundance (in log2 counts per million).
plotBCV(y, xlab="Average log CPM", ylab="Biological coefficient of variation",
pch=16, cex=0.2, col.common="red", col.trend="blue", col.tagwise="black", ...)y |
a |
xlab |
label for the x-axis. |
ylab |
label for the y-axis. |
pch |
the plotting symbol. See |
cex |
plot symbol expansion factor. See |
col.common |
color of line showing common dispersion |
col.trend |
color of line showing dispersion trend |
col.tagwise |
color of points showing genewise dispersions. Note that ‘tag’ and ‘gene’ are synonymous here. |
... |
any other arguments are passed to |
The BCV is the square root of the negative binomial dispersion. This function displays the common, trended and genewise BCV estimates.
A plot is created on the current graphics device.
Davis McCarthy, Yunshun Chen, Gordon Smyth
BCV.true <- 0.1 y <- DGEList(matrix(rnbinom(6000, size = 1/BCV.true^2, mu = 10),1000,6)) y <- estimateCommonDisp(y) y <- estimateTrendedDisp(y) y <- estimateTagwiseDisp(y) plotBCV(y)
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