bakR (version 1.0.1)

plotMA: Creating L2FC(kdeg) MA plot from fit objects

Description

This function outputs a L2FC(kdeg) MA plot. Plots are colored according to statistical significance and the sign of L2FC(kdeg)

Usage

plotMA(
  obj,
  Model = c("MLE", "Hybrid", "MCMC"),
  FDR = 0.05,
  Exps = 2,
  Exp_shape = FALSE
)

Value

A ggplot object. Each point represents a transcript. The x-axis is log-10 transformed replicate average read counts, y-axis is the log-2 fold-change in the degradation rate constant.

Arguments

obj

Object of class bakRFit outputted by bakRFit function

Model

String identifying implementation for which you want to generate an MA plot

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
plotMA(Fit, Model = "MLE")

# }