multiOmicsPlot_ORFikExp {RiboCrypt} | R Documentation

## Multi-omics plot using ORFik experiment input

### Description

Customizable html plots for visualizing genomic data.

### Usage

    multiOmicsPlot_ORFikExp(
      target_range,
      annotation = target_range,
      df,
      reference_sequence = findFa(df),
      reads = outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full"),
      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),
      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
`df` | an ORFik `experiment` or a list containing ORFik experiments. Usually a list when you have split Ribo-seq and RNA-seq etc.
`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. Default: `outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full")`
`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.
`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 1.0.0 Index]