frame_psite: Percentage of P-sites per reading frame.

In LabTranslationalArchitectomics/riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Percentage of P-sites per reading frame.

Description

This function computes, for each transcript region (5' UTR, coding sequence and 3' UTR), the percentage of P-sites falling in the three possible translation reading frames. It takes into account only transcripts with annotated regions of length > 0 and the resulting values are visualized as bar plots. Multiple samples and replicates can be handled.

Usage

frame_psite(
  data,
  annotation,
  sample,
  multisamples = "average",
  plot_style = "split",
  transcripts = NULL,
  region = "all",
  length_range = NULL,
  cl = 100,
  colour = NULL
)

Arguments

data	Either list of data tables or GRangesList object from psite_info.
annotation	Data table as generated by create_annotation.
sample	Either character string, character string vector or named list of character string(s)/character string vector(s) specifying the name of the sample(s) and replicate(s) of interest. If a list is provided, each element of the list is considered as an independent sample associated with one ore multiple replicates. Multiple samples and replicates are handled and visualised according to multisamples and plot_style.
multisamples	Either "average" or "independent". It specifies how to handle multiple samples and replicates stored in sample: if sample is a character string vector and multisamples is set to "average" the elements of the vector are considered as replicates of one sample and a single bar plot is returned. if sample is a character string vector and multisamples is set to "independent", each element of the vector is analysed independently of the others. The number of plots returned and their organization is specified by plot_style. if sample is a list, multisamples must be set to "average". Each element of the list is analysed independently of the others, its replicates averaged and its name reported in the plot. The number of plots returned and their organization is specified by plot_style. Note: when this parameter is set to "average" the bar plot associated with each sample displays the frame-specific mean signal computed across the replicates and the corresponding standard error is also reported. Default is "average".
plot_style	Either "split", "facet", "dodge" or "mirror". It specifies how to organize and display multiple bar plots: "split": one bar plot for each sample is returned as an independent ggplot object. "facet": the bar plots are placed one next to the other, in independent boxes. "dodge": all bar plots are displayed in one box and, for each frame, samples are placed side by side. "mirror": sample must be either a character string vector or a list of exactly two elements and the resulting bar plots are mirrored along the x axis. Default is "split".
transcripts	Character string vector listing the name of transcripts to be included in the analysis. Default is NULL, i.e. all transcripts are used.
region	Character string specifying the region(s) of the transcripts to be analysed. It can be either "5utr", "cds", "3utr", respectively for 5' UTRs, CDSs and 3' UTRs, or "all", i.e. all regions are considered. Note: according to this parameter the bar plots are differently arranged to optimise the organization and the visualization of the data.
length_range	Integer or integer vector for restricting the analysis to a chosen range of read lengths. Default is NULL, i.e. all read lengths are used.
cl	Integer value in 1,100 specifying a confidence level for restricting the analysis to an automatically-defined range of read lengths. The new range is computed according to the most frequent read lengths, which accounts for the cl% of the sample and is defined by discarding the (100-cl)% of read lengths falling in the tails of the read lengths distribution. If multiple sample names are provided, one range of read lengths is computed, such that at least the cl% of all samples is represented. Default is 100.
colour	Character string or character string vector specifying the colour of the bar plot(s). If plot_style is set to either "dodge" or "mirror", a colour for each sample is required. Default is NULL, i.e. the default R colour palette is used.

Value

List containing: one or more ggplot object(s) and the data table with the corresponding x- and y-axis values ("plot_dt"); an additional data table with raw and scaled number of P-sites per frame for each sample ("count_dt").

See Also

frame_psite_length for a similar plot stratified by read length.

Examples

## data(reads_list)
## data(mm81cdna)
##
## ## Generate fake samples and replicates
## for(i in 2:6){
##   samp_name <- paste0("Samp", i)
##   set.seed(i)
##   reads_list[[samp_name]] <- reads_list[["Samp1"]][sample(.N, 5000)]
## }
##
## ## Compute and add p-site details
## psite_offset <- psite(reads_list, flanking = 6, extremity = "auto")
## reads_psite_list <- psite_info(reads_list, psite_offset)
##
## ## Define the list of samples and replicate to use as input
## input_samples <- list("S1" = c("Samp1", "Samp2"),
##                       "S2" = c("Samp3", "Samp4", "Samp5"),
##                       "S3" = c("Samp6"))
##
## Generate bar plots
## example_frames <- frame_psite(reads_psite_list, mm81cdna,
##                               sample = input_samples,
##                               multisamples = "average",
##                               plot_style = "facet",
##                               region = "all",
##                               colour = c("#333f50", "#39827c", "gray70"))

LabTranslationalArchitectomics/riboWaltz documentation built on Jan. 17, 2024, 12:18 p.m.