n SNVs per chromosome plot

Visualizing the number of SNVs per chromosome.

fancy_snv_chrdistplot(
  this_sample_id,
  maf_data,
  maf_path = NULL,
  variant_type_col = 10,
  chromosome_col = 5,
  plot_title = paste0(this_sample_id),
  plot_subtitle = "SNV Distribution Per Chromosome",
  chr_select = paste0("chr", c(1:22)),
  include_dnp = FALSE,
  hide_legend = FALSE,
  coding_only = FALSE,
  from_flatfile = TRUE,
  use_augmented_maf = TRUE,
  this_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.

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).

plot_subtitle

Subtitle for created plot.

chr_select

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

include_dnp

Optional argument for including DNPs. Default is FALSE.

hide_legend

Set to True to remove legend from plot, default is FALSE.

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.

this_seq_type

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

Value

A plot as a ggplot object (grob).

Details

This function takes on an already loaded maf-like data frame, or a path to the maf file of interest. In addition, the user can also give this function a sample ID and the function will run assign_cn_to_ssm to get data for plotting. If a maf file or data frame is used, the user has the chance to specify what column that holds the Variant Type information (variant_type_col), in addition the user can also specify what column in the incoming maf that is corresponding to the chromosome annotations. This function also includes useful subsetting options. For example, chr_select allows the user to restrict the plot to specific chromosomes. include_dnp is an optional argument (Boolean) for if variants of this subtype should be included or not. The plot can also be restricted to only counting coding mutations (coding_only). Flat-file and augmented maf options can be toggled with from_flatfile and use_augmented_maf. Both are TRUE by default and should rarely be set to FALSE. Lastly, this plotting function also have convenient parameters for customizing the returned plot, e.g plot_title, y_interval, hide_legend, andplot_subtitle.

Examples

#plot SNVs
fancy_snv_chrdistplot(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
#> Warning: Removed 1 rows containing missing values (`position_stack()`).


#plot SNVs and DNPs
fancy_snv_chrdistplot(this_sample_id = "HTMCP-01-06-00422-01A-01D",
                      include_dnp = TRUE,
                      plot_subtitle = "SNV + DNP Distribution Per Chromosome")
#> 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()`).