plot_metagene: Plots the metagene coverage data

In mjgeng/ribor: An R Interface for Ribo Files

Description

The function plot_metagene plots the metagene site coverage, separating by experiment.

Usage

plot_metagene(
  x,
  site,
  experiment,
  range.lower,
  range.upper,
  normalize = FALSE,
  title = "Metagene Site Coverage",
  tick = 10
)

Arguments

x	A 'Ribo' object or a data frame generated from get_metagene
site	"start" or "stop" site
experiment	list of experiments
range.lower	lower bound of the read length, inclusive
range.upper	upper bound of the read length, inclusive
normalize	When TRUE, normalizes the data by the total reads.
title	title of the generated plot
tick	x-axis labeling increment

Details

If a DataFrame is provided as param 'x', then the only additional parameter is the optional title' parameter for the generated plot. If a ribo.object is provided as param 'x', the rest of the parameters listed are necessary.

When given a ribo class object, the plot_metagene function generates a DataFrame by calling the get_tidy_metagene function, so the run times in this case will be mostly comprised of a call to the get_metagene function.

This function uses ggplot in its underlying implementation.

Value

A 'ggplot' of the metagene site coverage

Examples

#a potential use case is to directly pass in the ribo object file as param 'x'

#generate the ribo object to directly use
file.path <- system.file("extdata", "sample.ribo", package = "ribor")
sample <- Ribo(file.path)

#specify experiments of interest
experiments <- c("Hela_1", "Hela_2", "WT_1")

#plot the metagene start site coverage for all experiments in 'sample.ribo'
#from read length 2 to 5
plot_metagene(x = sample,
              site = "start",
              range.lower = 2,
              range.upper = 5,
              experiment = experiments)

#Note that the site, range.lower, range.upper, and experiment parameter are only
#necessary if a ribo object is being passed in as param 'x'. If a ribo
#object is passed in, then the param 'experiments' will be set to all of
#the experiments by default.

#If a DataFrame is passed in, then the plot_metagene function
#does not need any other information. All of the elements of the DataFrame
#will be used, assuming that it contains the same column names and number of
#columns as the output from get_tidy_metagene()

#gets the metagene start site coverage from read length 2 to 5
#note that the data must be summed across transcripts and read lengths
#for the plot_metagene function
data <- get_tidy_metagene(sample,
                          site = "start",
                          range.lower = 2,
                          range.upper = 5)

#plot the metagene data
plot_metagene(data)

mjgeng/ribor documentation built on Dec. 21, 2021, 7:03 p.m.