bakR (version 1.0.1)

plotVolcano: Creating L2FC(kdeg) volcano plot from fit objects

Description

This function creates a L2FC(kdeg) volcano plot. Plots are colored according to statistical significance and sign of L2FC(kdeg).

Usage

plotVolcano(obj, FDR = 0.05, Exps = 2, Exp_shape = FALSE)

Value

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.

Arguments

obj

Object contained within output of bakRFit. So, either Fast_Fit (MLE implementation fit), Stan_Fit (MCMC implementation fit), or Hybrid_Fit (Hybrid implementation fit)

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

Examples

# \donttest{
# 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)

# }