plot_metagene_profiles: Plot metagene profiles

In ilia-kats/RiboSeqTools: Tools for analysis of selective ribosome profiling (SeRP) data

Description

Plots a metagene profile previously calculated with metagene_profiles. Lines show the real profile using all data, shading indicates a bootstrapping-based confdience interval.

Usage

plot_metagene_profiles(
  df,
  ylab,
  color,
  group,
  align = "start",
  ytrans = "identity",
  highlightregion = list(),
  highlightargs = list(),
  conf.level = 0.95,
  ci.alpha = 0.3
)

Arguments

df	A data frame created by metagene_profiles.
ylab	Y axis label.
color	Variable to use for the color scale. Defaults to exp, if a column exp exists in the data frame.
group	Additional grouping variable. Geoms will be grouped by color and group. Defaults to rep, if a column rep exists in the data frame.
align	Alignment to use in X axis label.
ytrans	Y axis transformation.
highlightargs	Named list of additional parameters to pass to annotate. Each list element will be recycled to match the number of annotations.
conf.level	Confidence level to plot.
ci.alpha	Transparency level for the CI shading.
exp	Experiments to plot. Defaults to all experiments.
higlightregion	Regions in the plot to be highlighted. Can be either a list containing two-element numeric vectors or a two-column matrix. Rectangles spanning the entire height of the plot will be drawn between the given x positions.

Value

A ggplot object.

Examples

## Not run: 
     plot_metagene_profiles(df, 'enrichment', exp, rep)

## End(Not run)

ilia-kats/RiboSeqTools documentation built on Oct. 5, 2020, 7:41 p.m.