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Sample-level Circos Plot

plot_sample_circos.Rd

Plot a sample-centric circos overview.

Usage

plot_sample_circos(
  this_sample_id,
  sv_df,
  cnv_df,
  ssm_df,
  include_sv = TRUE,
  include_ssm = FALSE,
  legend_metadata_columns,
  legend_metadata_names = c(),
  include_cnv = TRUE,
  genome_build,
  this_seq_type = "genome",
  chrom_list,
  label_genes,
  auto_label_sv = FALSE,
  link_colour_column = NULL,
  hide_legend = FALSE,
  verbose = FALSE
)

Arguments

this_sample_id

Sample ID for the sample to plot.

sv_df

Optional data frame of SVs. If not provided this function will run `get_manta_sv` to retrieve SVs.

cnv_df

Optional data frame of CNVs. If not provided, this function will run `get_sample_cn_segments` to retrieve CNVs.

ssm_df

This parameter does not do anything yet. Maybe it was meant to be implemented.

include_sv

Default TRUE. (does not do anything yet).

include_ssm

Defaul FALSE. (does not do anything yet).

legend_metadata_columns

Column names from metadata

legend_metadata_names

List of metadata names to be plotted.

include_cnv

Default TRUE. (does not do anything yet).

genome_build

genome_build to use (this is usually inferred automatically from your data)

this_seq_type

Seq type for returned CN segments. One of "genome" (default) or "capture".

chrom_list

List of chromosomes to be plotted. If not stated, chr1-22+X will be used.

label_genes

Gene labels (df, list or what type?)

auto_label_sv

Default is FALSE

Which column from sv_df to use for link colouring (default: NULL)

hide_legend

Set to TRUE if you want to suppress the legend. Particularly useful if you are not using GAMBL data/metadata

verbose

Set to TRUE for a chattier experience

Value

Nothing

Details

This function takes a sample ID in the `this_sample_id` parameter. Optionally, the user can supply already loaded data frames (SV, CNV, SSM) with the `sv_df`, `cnv_df` and `ssm_df` parameters. Convenient Boolean parameteers are also avaialble for restricting the plot to specific mutation types (`include_sv`, `include_cnv`, and `include_ssm`).

Examples

if (FALSE) { # \dontrun{
library(GAMBLR.open)

plot_sample_circos(this_sample_id = "02-13135T",
                   legend_metadata_columns = c("pathology",
                                               "lymphgen",
                                               "COO_consensus",
                                               "DHITsig_consensus"),
                   legend_metadata_names = c("pathology",
                                             "LymphGen",
                                             "COO",
                                             "DHITsig"),
                   chrom_list = c("chr3",
                                  "chr8",
                                  "chr14",
                                  "chr18"))
} # }