frame_psite_length: Percentage of P-sites per reading frame stratified by read...

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

Percentage of P-sites per reading frame stratified by read length.

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, stratified by read length. It takes into account only transcripts with annotated regions of length > 0 and the resulting values are visualized as heatmaps. Multiple samples and replicates can be handled in several ways.

Usage

frame_psite_length(
  data,
  annotation,
  sample,
  multisamples = "average",
  plot_style = "split",
  transcripts = NULL,
  region = "all",
  length_range = NULL,
  cl = 100,
  colour = "#172969"
)

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 multisample 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 multisample is set to "average" the elements of the vector are considered as replicates of one sample and a single heatmap is returned. if sample is a character string vector and multisample 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 list, multisample 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 heatmap associated with each sample displays the length- and frame- specific mean signal computed across the replicates. Default is "average".
plot_style	Either "split" or "facet". It specifies how to organize and display multiple heatmaps: "split": heatmap(s) for each sample are returned as an independent ggplot object. "facet": the heatmap(s) for each sample are placed one below the other (when region is "all") or one next to the other (when region is set to either "5utr", "cds", "3utr") in independent boxes. 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 heatmaps are differently arranged to optimise the organization and the visualization of the data.
length_range	Integer or integer vector for restricting the plot 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 plot 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 samples are analysed, a single range of read lengths is computed such that at least the cl% of all sample are represented. Default is 100.
colour	Character string specifying the colour of the plot. The colour scheme is as follow: tiles corresponding to the lowest signal are always white, tiles corresponding to the highest signal are of the specified colour and the progression between these two colours follows a linear gradient. Default is dark blue.

Value

List containing: one or more ggplot object(s) and the data table with the corresponding x- and y-axis values and the z-values, defining the color of the tiles ("plot_dt"); an additional data table with raw and scaled number of read extremities mapping around the start and the stop codon, per length, for each sample ("count_dt").

See Also

frame_psite for a similar plot where read lengths are collapsed.

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 heatmaps
## example_frames_stratified <- frame_psite_length(reads_psite_list, mm81cdna,
##                                                 sample = input_samples,
##                                                 multisamples = "average",
##                                                 plot_style = "split",
##                                                 region = "all",
##                                                 colour = "#333f50")

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