plot_sashimi {dasper} | R Documentation

## Visualise RNA-seq data in a the form of a sashimi plot

### Description

`plot_sashimi` plots the splicing events and coverage across specific genes/transcripts/regions of interest. Unlike traditional sashimi plots, coverage and junction tracks are separated, which enables user's to choose whether they would like to plot only the junctions.

### Usage

    plot_sashimi(
      junctions,
      ref,
      gene_tx_id,
      gene_tx_col,
      case_id = NULL,
      sum_func = mean,
      region = NULL,
      assay_name = "norm",
      annot_colour = c(ggpubr::get_palette("jco", 1), ggpubr::get_palette("npg", 7)[c(1, 3,
        2, 5, 6)], ggpubr::get_palette("jco", 6)[c(3)]),
      digits = 2,
      count_label = TRUE,
      coverage_paths_case = NULL,
      coverage_paths_control = NULL,
      coverage_chr_control = NULL,
      load_func = .coverage_load,
      binwidth = 100
    )

### Arguments

`junctions` | junction data as a RangedSummarizedExperiment-class object.
`ref` | either path to gtf/gff3 or object of class TxDb-class or EnsDb-class. EnsDb-class is required if you intend to annotate junctions with gene symbols/names.
`gene_tx_id` | character scalar with the id of the gene. This must be a an identifier for a gene or transcript, which has a matching entry in `ref`.
`gene_tx_col` | character scalar with the name of the column to search for the `gene_tx_id` in `ref`.
`case_id` | list containing 1 element. The contents of this element must be a character vector specifying sample ids that are to be plotted. The name of this element must correspond to the column containing sample ids in the junction `SummarizedExperiment::mcols()`. By default, all cases will be plotted.
`sum_func` | function that will be used to aggregate the junction counts and coverage for controls. By default, `mean` will be used.
`region` | a GenomicRanges of length 1 that is used to filter the exons/junctions plotted. Only those that overlap this region are plotted.
`assay_name` | a character scalar with the name of the `SummarizedExperiment::assay()` from which to obtain junction counts.
`annot_colour` | character vector length 7, representing the colours of junction types.
`digits` | used in `round()`, specifying the number of digits to round the junction counts to for visualisation purposes.
`count_label` | logical value specifying whether to add label the count of each junction.
`coverage_paths_case` | paths to the BigWig files containing the coverage of your case samples.
`coverage_paths_control` | paths to the BigWig files for control samples.
`coverage_chr_control` | either "chr" or "no_chr", indicating the chromosome format of control coverage data. Only required if the chromosome format of the control BigWig files is different to that of your cases.
`load_func` | function used to load coverage.
`binwidth` | the number of bases to aggregate coverage across using `sum_func` when plotting. .

### Value

`ggplot` displaying the splicing (and coverage) surrounding the transcript/region of interest.

### Examples

    # use GenomicState to load txdb (GENCODE v31)
    ref <- GenomicState::GenomicStateHub(
        version = "31",
        genome = "hg38",
        filetype = "TxDb"
    )[[1]]

    junctions_processed <- junction_process(
        junctions_example,
        ref,
        types = c("ambig_gene", "unannotated")
    )

    sashimi_plot <- plot_sashimi(
        junctions = junction_filter(junctions_processed),
        ref = ref,
        gene_tx_id = "ENSG00000142156.14",
        gene_tx_col = "gene_id",
        sum_func = NULL
    )

[Package dasper version 1.4.0 Index]