plot_metagene {ribor} | R Documentation |
The function plot_metagene
plots the metagene site coverage,
separating by experiment.
plot_metagene( x, site, experiment, range.lower, range.upper, normalize = FALSE, title = "Metagene Site Coverage", tick = 10 )
x |
A 'Ribo' object or a data frame generated from |
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 |
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.
A 'ggplot' of the metagene site coverage
#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)