| plot_region_counts {ribor} | R Documentation |
The function plot_region_counts can take either a DataFrame
or a "Ribo" object to generate the a stacked bar plot of proportions that
correspond to the "UTR5", "CDS", and "UTR3" regions.
plot_region_counts( x, experiment, range.lower, range.upper, title = "Region Counts" )
x |
A 'Ribo' object or a DataFrame generated from |
experiment |
a list of experiment names |
range.lower |
a lower bounds for a read length range |
range.upper |
an upper bounds for a read length range |
title |
a title for the generated plot |
When given a 'Ribo' object, plot_region_counts calls
get_region_counts to retrieve the necessary information
for plotting. This option is in the case that a DataFrame of the
region count information is not required.
The user can instead provide a DataFrame with the same structure as the
output of the get_region_counts function where the 'transcript'
and 'length' parameters are the default values of TRUE. This also means that
the remaining parameters of the plot_region_counts function are not necessary.
The run time becomes substantially faster when plot_region_counts is given
the direct DataFrame to plot. However, the DataFrame needs to follow the format and
types in the output of the reading functions
A 'ggplot' of the region counts for each of the experiments
get_region_counts to generate a DataFrame that can be provided as input,
Ribo to create a ribo.object that can be provided as input
#ribo object use case
#generate the ribo object
file.path <- system.file("extdata", "sample.ribo", package = "ribor")
sample <- Ribo(file.path)
#specify the regions and experiments of interest
regions <- c("UTR5", "CDS", "UTR3")
experiments <- c("Hela_1", "Hela_2", "WT_1")
plot_region_counts(sample,
range.lower = 2,
range.upper = 5,
experiments)
#DataFrame use case
#obtains the region counts at each individual read length, summed across every transcript
region.counts <- get_region_counts(sample,
region = regions,
range.lower = 2,
range.upper = 5,
tidy = TRUE,
length = TRUE,
transcript = TRUE)
#the params 'length' and 'transcript' must be set to true to use a DataFrame
plot_region_counts(region.counts)