DEG.plot.static: Plot DEG result

In Roleren/ORFik: Open Reading Frames in Genomics

Plot DEG result

Description

Plot setup:
X-axis: mean counts Y-axis: Log2 fold changes For explanation of plot, see DEG.analysis

Usage

DEG.plot.static(
  dt,
  output.dir = NULL,
  p.value.label = 0.05,
  plot.title = "",
  plot.ext = ".pdf",
  width = 6,
  height = 6,
  dot.size = 0.4,
  xlim = "auto",
  ylim = "bidir.max",
  relative.name = paste0("DEG_plot", plot.ext)
)

Arguments

dt	a data.table with the results from DEG.analysis
output.dir	a character path, default NULL(no save), or a directory to save to a file. Relative name of file, specified by 'relative.name' argument.
p.value.label	a numeric, default 0.05 in interval (0,1) or "" to not show. What p-value used for the analysis? Will be shown as a caption.
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	numeric, default 6 (in inches)
dot.size	numeric, default 0.4, size of point dots in plot.
xlim	numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of meanCounts column in dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max x limit: like c(-5, 5)
ylim	numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of LFC column in dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max y limit: like c(-10, 10)
relative.name	character, Default: paste0("DEG_plot", plot.ext) Relative name of file to be saved in folder specified in output.dir. Change to .pdf if you want pdf file instead of png.

Value

a ggplot object

See Also

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

Examples

df <- ORFik.template.experiment()
df.rna <- df[df$libtype == "RNA",]
#dt <- DEG.analysis(df.rna)
#Default scaling
#DEG.plot.static(dt)
#Manual scaling
#DEG.plot.static(dt, xlim = c(-2, 2), ylim = c(-2, 2))

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.