plotVolcano {bakR} | R Documentation |
This function creates a L2FC(kdeg) volcano plot. Plots are colored according to statistical significance and sign of L2FC(kdeg).
plotVolcano(obj, FDR = 0.05, Exps = 2, Exp_shape = FALSE)
obj |
Object contained within output of |
FDR |
False discovery rate to control at for significance assessment |
Exps |
Vector of Experimental IDs to include in plot; must only contain elements within 2:(# of experimental IDs). If NULL, data for all Experimental IDs is plotted. |
Exp_shape |
Logical indicating whether to use Experimental ID as factor determining point shape in volcano plot |
A ggplot object. Each point represents a transcript. The x-axis is the log-2 fold change in the degradation rate constant and the y-axis is the log-10 transformed multiple test adjusted p value.
# Simulate data for 500 genes and 2 replicates
sim <- Simulate_bakRData(500, nreps = 2)
# Fit data with fast implementation
Fit <- bakRFit(sim$bakRData)
# Volcano plot
plotVolcano(Fit$Fast_Fit)