Mutation Frequency Heatmap — get_mutation_frequency_bin

Count hypermutated bins and generate heatmap/cluster the data.

get_mutation_frequency_bin_matrix(
  regions,
  regions_df,
  these_samples_metadata,
  seq_type = "genome",
  region_padding = 1000,
  metadataColumns = c("pathology"),
  sortByColumns = c("pathology"),
  expressionColumns = c(),
  orientation = "sample_rows",
  skip_regions = c("MYC", "BCL2", "IGLL5"),
  customColour = NULL,
  slide_by = 100,
  window_size = 500,
  min_count_per_bin = 3,
  min_bin_recurrence = 5,
  min_bin_patient = 0,
  region_fontsize = 8,
  cluster_rows_heatmap = FALSE,
  cluster_cols_heatmap = FALSE,
  show_gene_colours = FALSE,
  legend_row = 3,
  legend_col = 3,
  legend_direction = "horizontal",
  legendFontSize = 10,
  from_indexed_flatfile = TRUE,
  mode = "slms-3"
)

Arguments

regions: Vector of regions in the format "chr:start-end".
regions_df: Data frame of regions with four columns (chrom,start,end,gene_name).
these_samples_metadata: GAMBL metadata subset to the cases you want to process (or full metadata).
seq_type: The seq_type you want back, default is genome.
region_padding: How many bases will be added on the left and right of the regions to ensure any small regions are sufficiently covered by bins. Default is 1000.
metadataColumns: What metadata will be shown in the visualization.
sortByColumns: Which of the metadata to sort on for the heatmap.
expressionColumns: Optional variable for retrieving expression values for a specific gene(s).
orientation: Specify the sample orientation, default is sample_rows.
skip_regions: Regions to be filtered out from the regions data frame. Only applies if regions_df is not provided. Default is MYC, BCL2 and IGLL5.
customColour: Optional named list of named vectors for specifying all colours for metadata. Can be generated with map_metadata_to_colours. Default is NULL.
slide_by: How far to shift before starting the next window.
window_size: The width of your sliding window.
min_count_per_bin: Minimum counts per bin, default is 3.
min_bin_recurrence: How many samples a bin must be mutated in to retain in the visualization.
min_bin_patient: How many bins must a patient mutated in to retain in the visualization.
region_fontsize: Font size of regions in plot, default is 8ppt.
cluster_rows_heatmap: Optional parameter to enable/disable clustering of each dimension of the heatmap. Default is FALSE.
cluster_cols_heatmap: Optional parameter to enable/disable clustering of each dimension of the heatmap. Default is FALSE.
show_gene_colours: Optional logical argument indicating whether regions should have associated colours plotted as annotation track of heatmap.
legend_row: Fiddle with these to widen or narrow your legend.
legend_col: Fiddle with these to widen or narrow your legend.
legend_direction: Accepts one of "horizontal" (default) or "vertical" to indicate in which direction the legend will be drawn.
legendFontSize: Font size of legend in plot, default is 10ppt.
from_indexed_flatfile: Set to TRUE to avoid using the database and instead rely on flat files (only works for streamlined data, not full MAF details).
mode: Only works with indexed flat files. Accepts 2 options of "slms-3" and "strelka2" to indicate which variant caller to use. Default is "slms-3".

Value

Nothing

Details

This function takes a metadata table with these_samples_metadata parameter and internally calls calc_mutation_frequency_sliding_windows (that internally calls get_ssm_by_regions) to retrieve mutations for plotting. This plotting function has a variety of useful parameters, providing many customizable plotting options. For more details on how these parameters can be used, and extended usage examples, refer to the SSM tutorial vignette section 1.4.9.

Examples

#load metadata.
metadata = get_gambl_metadata()
dlbcl_bl_meta = dplyr::filter(metadata, pathology %in% c("DLBCL", "BL"))

#bring together all derived sample-level results from many GAMBL pipelines.
dlbcl_bl_meta = collate_results(join_with_full_metadata = TRUE,
                                these_samples_metadata = dlbcl_bl_meta)
#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
#> Joining with `by = join_by(patient_id, sample_id, biopsy_id)`

#get ashm regions
some_regions = grch37_ashm_regions
#> Error in eval(expr, envir, enclos): object 'grch37_ashm_regions' not found

get_mutation_frequency_bin_matrix(these_samples_metadata = dlbcl_bl_meta,
                                  regions_df = some_regions)
#> Error in apply(regions_df, 1, function(x) {    paste0(x[1], ":", as.numeric(x[2]) - region_padding, "-",         as.numeric(x[3]) + region_padding)}): object 'some_regions' not found