multiOmicsPlot_ORFikExp: Multi-omics plot using ORFik experiment input

In m-swirski/RiboCrypt: Interactive visualization in genomics

Multi-omics plot using ORFik experiment input

Description

Customizable html plots for visualizing genomic data.

Usage

multiOmicsPlot_ORFikExp(
  display_range,
  df,
  annotation = "cds",
  reference_sequence = findFa(df),
  reads = outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full",
    BPPARAM = BiocParallel::SerialParam()),
  viewMode = c("tx", "genomic")[1],
  custom_regions = NULL,
  leader_extension = 0,
  trailer_extension = 0,
  withFrames = libraryTypes(df, uniqueTypes = FALSE) %in% c("RFP", "RPF", "LSU"),
  frames_type = "lines",
  colors = NULL,
  kmers = NULL,
  kmers_type = c("mean", "sum")[1],
  ylabels = bamVarName(df),
  lib_to_annotation_proportions = c(0.8, 0.2),
  lib_proportions = NULL,
  annotation_proportions = NULL,
  width = NULL,
  height = NULL,
  plot_name = "default",
  plot_title = NULL,
  display_sequence = c("both", "nt", "aa", "none")[1],
  seq_render_dist = 100,
  aa_letter_code = c("one_letter", "three_letters")[1],
  annotation_names = NULL,
  start_codons = "ATG",
  stop_codons = c("TAA", "TAG", "TGA"),
  custom_motif = NULL,
  log_scale = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  input_id = "",
  summary_track = FALSE,
  summary_track_type = frames_type,
  export.format = "svg"
)

Arguments

display_range	the whole region to visualize, a GRangesList or GRanges object
df	an ORFik experiment or a list containing ORFik experiments. Usually a list when you have split Ribo-seq and RNA-seq etc.
annotation	the whole annotation which your target region is a subset, a GRangesList or GRanges object
reference_sequence	the genome reference, default ORFik::findFa(df)
reads	the NGS libraries, as a list of GRanges with or without 'score' column for replicates. Can also be a covRle object of precomputed coverage. Default: outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full", BPPARAM = BiocParallel::SerialParam())
viewMode	character, default "tx" (transcript coordinates, first position is 1, exons are merged into a single sequence) Alternative: "genomic" (genomic coordinates, first position is first position in display_range argument. Introns are displayed).
custom_regions	a GRangesList or NULL, default: NULL. The alternative annotation, like self defined uORFs etc. The vertical annotation bars will have a different color.
leader_extension	integer, default 0. (How much to extend view upstream)
trailer_extension	integer, default 0. (How much to extend view downstream)
withFrames	a logical vector, default libraryTypes(df, uniqueTypes = FALSE) %in% c("RFP", "RPF", "LSU") 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 bamVarName(df). Name of libraries in "reads" list argument.
lib_to_annotation_proportions	numeric vector of length 2. relative sizes of profiles and annotation.
lib_proportions	numeric vector of length equal to displayed libs. Relative sizes of profiles displayed
annotation_proportions	numeric vector of length 3 (seq displayed), or 2 (seq not displayed). Relative sizes of annotation tracks.
width	numeric, default NULL. Width of plot.
height	numeric, default NULL. Height of plot.
plot_name	character, default "default" (will create name from display_range name).
plot_title	character, default NULL. A title for plot.
display_sequence	character/logical, default c("both","nt", "aa", "none")[1]. If TRUE or "both", display nucleotide and aa sequence in plot.
seq_render_dist	integer, default 100. The sequences will appear after zooming below this threshold.
aa_letter_code	character, when set to "three_letters", three letter amino acid code is used. One letter by default.
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.
log_scale	logical, default FALSE. Log2 scale the count values, for easier visualization of shapes.
BPPARAM	how many cores/threads to use? default: BiocParallel::SerialParam(). To see number of threads used for multicores, do BiocParallel::bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.
input_id	character path, default: "", id for shiny to disply structures, should be "" for local users.
summary_track	logical, default FALSE. Display a top track, that is the sum of all tracks.
summary_track_type	character, default is same as 'frames_type' argument
export.format	character, default: "svg". alternative: "png". when you click the top right image button export, what should it export as?

Value

the plot object

Examples

library(RiboCrypt)
df <- ORFik.template.experiment()[9,] #Use third library in experiment only
cds <- loadRegion(df, "cds")
multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[1], 30), 30), df = df,
                        frames_type = "columns")

m-swirski/RiboCrypt documentation built on April 16, 2024, 10:21 p.m.