Description Usage Arguments Value Author(s)
A topTable volcano plot. Volcano plot of a toptable -
similar to volcanoplot
from
limma
, but more flexible in terms of what is
plotted on the y-axis.
1 2 3 4 5 6 7 | volcanoplot_topTable(tt, yaxis = c("p", "q", "B", "t"),
xaxis = c("logFC", "signedFC", "FC"), yThresh = 0.05,
lfc = log2(1.5), highlight = 0, names = tt$ID,
main = "Volcano Plot", cex.points = 0.2, ablines = "",
abline.col = "grey", colour.scheme = "red",
xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL,
do.par = TRUE, ...)
|
tt |
a |
yaxis |
choose one of “p”, “q”, “B”, “t”, “absT” to plot the raw P-values, the q value (either from a column called “q”, or “adj.P.Val” in that order), the B statistics (log odds), the t-statistic, or the absolute t-statistic, respectively. |
xaxis |
the x-axis type. one of: “logFC”
(default), “signedFC” (see
|
yThresh |
For colouring significant points. For eg, choose 0.05 for P/q, or 3 for B, or 5 for t |
lfc |
the absolute log fold change threshold. eg 0.585 for 1.5 FC, or 1.0 for a 2-fold change |
highlight |
the number of points to highlight by name |
names |
the names to use if highlight > 0. This
should have as many rows as were passed into
|
main |
the plot title. |
cex.points |
see |
ablines |
whether to add vertical dashed lines at
|
abline.col |
the colour of the ablines, if
|
colour.scheme |
Control the higlighting of DE genes, via either black/red dots (“red”) or closed/open circles(“black”) |
xlim |
see |
ylim |
see |
xlab |
The x-axis label. if |
ylab |
The y-axis label. if |
do.par |
logical: setup the plot parameters |
... |
further arguments passed to
|
nothing
Mark Cowley, 2008-07-25
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