n variants per chromosome plot. — fancy_v

Visualizing variant (SSM or SVs) counts per chromosome.

fancy_v_chrcount(
  this_sample_id,
  maf_data,
  maf_path = NULL,
  ssm = TRUE,
  projection = "grch37",
  min_vaf = 0,
  variant_type_col = 10,
  chromosome_col = 5,
  plot_title = paste0(this_sample_id),
  y_interval = 1,
  hide_legend = FALSE,
  plot_subtitle = "Variant Count Distribution Per Chromosome",
  chr_select = paste0("chr", c(1:22)),
  coding_only = FALSE,
  from_flatfile = TRUE,
  use_augmented_maf = TRUE,
  add_qc_metric = FALSE,
  seq_type = "genome"
)

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)
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).
plot_title: Title of plot (default to sample ID).
y_interval: Optional parameter for specifying intervals on y-axis.
hide_legend: Set to True to remove legend from plot, default is FALSE.
plot_subtitle: Subtitle for created plot.
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.
add_qc_metric: Boolean statement, if set to TRUE specified QC metric will be added (second y-axis).
seq_type: Default is "genome".

Value

A plot as a ggplot object (grob).

Details

Takes a maf data frame (or path to a maf), counts the number of variants per chromosome. Selected chromosomes (chr_select) are plotted along the x-axis and the variant counts are represented on the y-axis. This function can plot both Structural Variants (SV) and Simple Shared Motifs (SSM). It plots SVs per default and SSM can be added with setting ssm = TRUE. This plot can also be restricted to only show coding mutations. To do so, set coding_only to TRUE. In addition, the returned plot can also be superimposed with a sample-specific mean coverage (from collate_results). To do so, set add_qc_metric to TRUE. A collection of parameters for customizing the returned plot are also available. e.g plot_title, y_interval, hide_legend, and plot_subtitle.

Examples

#plot ssm
fancy_v_chrcount(this_sample_id = "HTMCP-01-06-00422-01A-01D",
                 ssm = TRUE)
#> 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
#> Warning: Removed 2 rows containing missing values (`position_stack()`).


#plot SVs for chr 1-5
fancy_v_chrcount(this_sample_id = "HTMCP-01-06-00422-01A-01D",
                 ssm = FALSE,
                 min_vaf = 0,
                 projection = "grch37",
                 chr_select = paste0("chr", c(1:5)),
                 plot_subtitle = "SV Count Distribution (chr1-5)")
#> Warning: number of columns of result is not a multiple of vector length (arg 3)
#> Warning: Removed 18 rows containing missing values (`position_stack()`).