Description Usage Arguments Details Value Examples
volcanoPlot
Make an expression volcano plot
from log2-fold change and p-value data
1 2 3 4 |
pval |
A vector of p-values |
lfc |
A vector of log-2 fold change (or similar data) |
sig |
Either a 0/1 binary vector of significance, or a vector of transformed p-values |
alpha |
If providing a vector of transformed p-values, this specifies the threshold for siginficance. Otherwise, not used. |
pointcols |
Vector of legnth 2. The first element indicates the color of significant points and the second the non sigificant points |
pchs |
Follows pointcols for point shapes |
cex |
Follows pointcols for point sizes |
legpos |
The position of the legend. Defaults to topright |
leginset |
How much the legend should be inset - defaults to just outside the plotting window. |
ylab |
The label for the y axis |
xlab |
The label for the x axis |
... |
additional arguments passed on to plot |
Using base R graphics, this function tabulates the number of significant values and plots
a table with the number and direction of significance
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
data(kidney) #from the simseq package
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-data.frame(rep=kidney$replic, treatment=kidney$treatment)
stats<-pipeLIMMA(counts=counts, info=info,
formula = " ~ treatment",
block=NULL,
getTopTable=T,
getEbayes=T)
stats<-stats$stats
volcanoPlot(pval=stats$ebayesPvalue_treatmentTumor,
lfc=stats$treatmentTumor_logFC,
sig=stats$ebayesQvalue_treatmentTumor,
alpha=0.0005, pointcols=c("blue","grey"), pchs=c(4,6))
## End(Not run)
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