te_rna.plot: Translational efficiency plots

In JokingHero/ORFik: Open Reading Frames in Genomics

Translational efficiency plots

Description

Create TE plot of:
- Within sample (TE log2 vs mRNA fpkm)

Usage

te_rna.plot(
  dt,
  output.dir = NULL,
  filter.rfp = 1,
  filter.rna = 1,
  plot.title = "",
  plot.ext = ".pdf",
  width = 6,
  height = "auto",
  dot.size = 0.4,
  xlim = c(filter.rna, filter.rna + 2.5)
)

Arguments

dt	a data.table with the results from te.table
output.dir	a character path, default NULL(no save), or a directory to save to a file will be called "TE_within.pdf"
filter.rfp	numeric, default 1. What is the minimum fpkm value?
filter.rna	numeric, default 1. What is the minimum fpkm value?
plot.title	title for plots, usually name of experiment etc
plot.ext	character, default: ".pdf". Alternatives: ".png" or ".jpg".
width	numeric, default 6 (in inches)
height	a numeric, width of plot in inches. Default "auto".
dot.size	numeric, default 0.4, size of point dots in plot.
xlim	numeric vector of length 2. X-axis limits. Default: c(filter.rna, filter.rna + 2.5)

Value

a ggplot object

See Also

Other DifferentialExpression: DEG.plot.static(), DEG_model(), DTEG.analysis(), DTEG.plot(), te.table()

Examples

df <- ORFik.template.experiment()
df.rfp <- df[df$libtype == "RFP",]
df.rna <- df[df$libtype == "RNA",]
#dt <- te.table(df.rfp, df.rna)
#te_rna.plot(dt, filter.rfp = 0, filter.rna = 5, dot.size = 1)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.