Rainfall Plot

Plot a rainfall plot for one sample. This function takes in the MAF data frame, or path to a custom MAF file.

Usage

prettyRainfallPlot(
  this_sample_id = NULL,
  label_ashm_genes = TRUE,
  projection = "grch37",
  chromosome,
  sv_data = NULL,
  this_maf = NULL,
  maf_path,
  zoom_in_region,
  this_seq_type,
  label_sv = FALSE,
  plot_title,
  annotate_sv = TRUE
)

Arguments

this_sample_id

Sample id for the sample to display. This is argument is not required if you want a multi-sample plot but is otherwise needed.

label_ashm_genes

Boolean argument indicating whether the aSHM regions will be labeled or not.

projection

Specify projection (grch37 or hg38) of mutations. Default is grch37.

chromosome

Provide one or more chromosomes to plot. The chr prefix can be inconsistent with projection and will be handled.

sv_data

Optionally provide the SV data to be used for plotting instead of retreiving SVs through GAMBLR on the fly.

this_maf

Specify custom MAF data frame of mutations.

maf_path

Specify path to MAF file if it is not already loaded into data frame.

zoom_in_region

Provide a specific region in the format "chromosome:start-end" to zoom in to a specific region.

this_seq_type

Specify one of "genome" or "capture" when relying on the function to obtain mutations from a region (i.e. if you haven't provided a MAF or single sample_id)

label_sv

Boolean argument to specify whether label SVs or not with green line on rainfall plot.

plot_title

Specify the title for the returned plot, default is the provided sample_id

annotate_sv

Optionally annotate intrachromosomal SVs to label the gene and partner information on the plot. Default is TRUE (perform annotation).

Value

a ggplot2 object

Details

Create a sample-level rainfall plot visualizing single nucleotide substitutions mutations for selected chromosomes.

Examples

suppressMessages(library(GAMBLR.open))
maf = GAMBLR.data::sample_data$grch37$maf
prettyRainfallPlot(this_sample_id = "14-35026",
                   this_maf = maf,
                   label_sv = FALSE,
                   chromosome = "3")
#> Subsetting MAF to the specified sample ...


if (FALSE) { # \dontrun{
# This mode will annotate and label SVs
prettyRainfallPlot(
     this_sample_id = "DOHH-2",
     this_seq_type = "genome",
     zoom_in_region = "8:125252796-135253201",
     label_sv = TRUE
)

# Will not annotate SVs (use raw bedpe) but still label them
prettyRainfallPlot(
     this_sample_id = "DOHH-2",
     this_seq_type = "genome",
     zoom_in_region = "8:125252796-135253201",
     label_sv = TRUE,
     annotate_sv = FALSE
)

# Will use user-specified SV data
sv <- get_manta_sv(
    these_sample_ids = "DOHH-2"
)

prettyRainfallPlot(
     this_sample_id = "DOHH-2",
     this_seq_type = "genome",
     zoom_in_region = "8:125252796-135253201",
     sv_data = sv,
     label_sv = TRUE
)
} # }