multiOmicsPlot_list {RiboCrypt}R Documentation

Multi-omics plot using list input

Description

Customizable html plots for visualizing genomic data.

Usage

multiOmicsPlot_list(
  target_range,
  annotation = target_range,
  reference_sequence,
  reads,
  withFrames = NULL,
  frames_type = "lines",
  colors = NULL,
  kmers = NULL,
  kmers_type = c("mean", "sum")[1],
  ylabels = NULL,
  proportions = NULL,
  width = NULL,
  height = NULL,
  plot_name = "default",
  plot_title = NULL,
  display_sequence = FALSE,
  annotation_names = NULL,
  start_codons = "ATG",
  stop_codons = c("TAA", "TAG", "TGA"),
  custom_motif = NULL,
  BPPARAM = bpparam()
)

Arguments

target_range

the whole region to visualize, a GRangesList or GRanges object

annotation

the whole annotation which your target region is a subset, a GRangesList or GRanges object

reference_sequence

the genome reference, a FaFile or FaFile convertible object

reads

the NGS libraries, as a list of GRanges with or without score column for replicates.

withFrames

a logical vector, default NULL. Alternative: a length 1 or same length as list length of "reads" argument.

frames_type

character, default "lines". Alternative:
- columns
- stacks
- area

colors

character, default NULL (automatic colouring). If "withFrames" argument is TRUE, colors are set to to c("red", "green", "blue") for the 3 frames. Alternative: Character vector of length 1 or length of "reads" list argument.

kmers

numeric (integer), bin positions into kmers.

kmers_type

character, function used for kmers sliding window. default: "mean", alternative: "sum"

ylabels

character, default NULL. Name of libraries in "reads" list arugment.

proportions

numeric, default NULL. Width of plot.

width

numeric, default NULL. Width of plot.

height

numeric, default NULL. Height of plot.

plot_name

= character, default "default" (will create name from target_range name). Alternative: custom name for region.

plot_title

character, default NULL. A title for plot.

display_sequence

logical, default FALSE. If TRUE, display nucleotide sequence in plot.

annotation_names

character, default NULL. Alternative naming for annotation.

start_codons

character vector, default "ATG"

stop_codons

character vector, default c("TAA", "TAG", "TGA")

custom_motif

character vector, default NULL.

BPPARAM

how many cores/threads to use? default: BiocParallel::bpparam(). To see number of threads used, do BiocParallel::bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.

Value

the plot object

Examples

library(ORFik)
df <- ORFik.template.experiment()[3,] #Use third library in experiment only
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19")) {
  cds <- loadRegion(df, "cds")
  multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[1], 30), 30), df = df,
                        reference_sequence = BSgenome.Hsapiens.UCSC.hg19::Hsapiens,
                        frames_type = "columns")
}

[Package RiboCrypt version 0.99.10 Index]