plotTE: Plot translational efficiency
In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

plotTE

R Documentation

Plot translational efficiency

Description

Scatterplot of RNA/RPFs level compared to the translational efficiency.

Usage

plotTE(
  TE,
  sample,
  xaxis = c("mRNA", "RPFs"),
  removeZero = TRUE,
  log2 = TRUE,
  theme = theme_classic(),
  type = "histogram",
  margins = "y",
  ...
)

Arguments

`TE`	Output of translationalEfficiency
`sample`	Sample names to plot.
`xaxis`	What to plot for x-axis.
`removeZero`	Remove the 0 values from plots.
`log2`	Do log2 transform for TE or not.
`theme`	Theme for ggplot2.
`type`, `margins`, `...`	Parameters pass to ggMarginal

Value

A ggExtraPlot object.

Examples

path <- system.file("extdata", package="ribosomeProfilingQC")
#RPFs <- dir(path, "RPF.*?\.[12].bam$", full.names=TRUE)
#RNAs <- dir(path, "mRNA.*?\.[12].bam$", full.names=TRUE)
#gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
#cnts <- countReads(RPFs, RNAs, gtf, level="gene")
cnts <- readRDS(file.path(path, "cnts.rds"))
fpkm <- getFPKM(cnts)
te <- translationalEfficiency(fpkm)
plotTE(te, 1)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.