Variant size distribution plot

Generate a violin plot showing variant (SSM or SVs) size distributions for selected contigs.

fancy_v_sizedis(
  this_sample_id,
  maf_data,
  maf_path = NULL,
  ssm = TRUE,
  projection = "grch37",
  this_seq_type = "genome",
  min_vaf = 0,
  variant_type_col = 10,
  chromosome_col = 5,
  start_col = 6,
  end_col = 7,
  plot_title = paste0(this_sample_id),
  plot_subtitle = "Variant Size Distribution",
  scale_value = "width",
  log_10 = TRUE,
  plot_trim = FALSE,
  chr_select = paste0("chr", c(1:22)),
  coding_only = FALSE,
  from_flatfile = TRUE,
  use_augmented_maf = TRUE
)

Arguments

this_sample_id

Sample to be plotted.

maf_data

Optional parameter with maf like df already loaded into R.

maf_path

Optional parameter with path to external maf like file.

ssm

Set to FALSE to get plotting data from get_combined_sv (SVs). Default value is TRUE (plots SSM retrieved from annotate_cn_by_ssm$maf).

projection

Genome build for returned variants (only applicable for ssm = FALSE).

this_seq_type

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

min_vaf

The minimum tumour VAF for a SV to be returned. Recommended: 0 (only applicable for ssm = FALSE).

variant_type_col

Index of column holding Variant Type (to be used with either maf_data or maf_path).

chromosome_col

Index of column holding Chromosome (to be used with either maf_data or maf_path).

start_col

Index of column with variant start coordinates (to be used with either maf_data or maf_path).

end_col

Index of column with variant end coordinates (to be used with either maf_data or maf_path).

plot_title

Title of plot (default to sample ID).

plot_subtitle

Subtitle for created plot.

scale_value

Scale type for violin plot, accepted values are "area", "width", and "count", default is "count.

log_10

Boolean statement for y-axis, default is TRUE.

plot_trim

If TRUE, trim the tails of the violins to the range of the data. If FALSE (default), don't trim the tails.

chr_select

vector of chromosomes to be included in plot, defaults to autosomes.

coding_only

Optional. Set to TRUE to restrict to plotting only coding mutations.

from_flatfile

If set to true the function will use flat files instead of the database.

use_augmented_maf

Boolean statement if to use augmented maf, default is FALSE.

Value

A plot as a ggplot object (grob).

Details

Function for plotting variant size distributions. This function takes either a sample ID given to the this_sample parameter. In addition, the function can also accept an already loaded MAF or MAF-like object given to the maf_data parameter. As a third option, the function can also read a maf from disk (provide path to maf with maf_path). A collection of convenient filtering and data subsetting parameters are also available for this function. For restricting your data (if plotting data retrieved with this_sample_id), the user can choose to only plot coding mutations with setting coding_only to TRUE. This plot can also deal with SVs as well as SSM data. To control this, please use the ssm parameter. If set to TRUE and if this_sample is called, the function gets data with annotate_cn_by_ssm and if set to FALSE, the function calls get_combined_sv to get SV calls for plotting. If the user calls either maf_data or maf_path, there are a collection of parameters available for specifying the relevant columns in the given data frame (variant_type_col, chhromosome_col, start_col, end_col). It is also possible to restrict the returned plot to any given chromosome. This is done with the chr_select parameter (default is all autosomes). In addition, plot aesthetics can also be controlled with plot_title, plot_subtitle, scale_value, log10, and trim. For more info on how to run with these parameters, refer to the parameter descriptions.

Examples

#plot SSM size distributions:
fancy_v_sizedis(this_sample_id = "HTMCP-01-06-00422-01A-01D")
#> trying to find output from: battenberg
#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg