Comut Plot — comut • ComutR

Comut Plot

Usage

comut(
  data,
  metadata,
  variant_colors,
  variant_scheme,
  show_variant_legend = TRUE,
  col_maps,
  features_of_interest,
  text_annotation,
  text_annotation_col = "white",
  text_annotation_size = 8,
  barplot_data,
  grob = FALSE,
  body_width,
  body_height,
  body_border = FALSE,
  cell_height = 0.25,
  cell_width = 0.25,
  legend_side = "right",
  legend_fontsize = 10,
  anno_fontsize = 8,
  add_borders = FALSE,
  show_barcodes = TRUE,
  id_order,
  ids,
  ...
)

Arguments

data: df with Tumor_Sample_Barcode, Hugo_Symbol, Variant_Classification, and optional column for text annotations
metadata: df with Tumor_Sample_Barcode, and metadata columns
variant_colors: colorscheme for alteration types, named list
variant_scheme: naming scheme to convert alteration types. If provided should match variant_colors names
show_variant_legend: whether the legend of variant types should be include. Default is TRUE.
col_maps: named list of color maps. Names should match columns of metadata
features_of_interest: optional vector of genes of interest
text_annotation: How to annotate comut plot squares if desired, must be a column in data
text_annotation_col: Size of text annotations, default is 8.
text_annotation_size: Color of text annotations, default is white.
barplot_data: named list of named lists. Each sub list should contain data, colors, and legend params for plots
grob: whether to return grob object instead of plotting. Useful for other frameworks.
body_width: width of the heatmap body in inches.
body_height: height of the heatmap body in inches.
body_border: boolean to add border to comut body.
cell_height: height of the heatmap cells. Also applies to annotations.
cell_width: width of the heatmap cells.
legend_side: side of heatmap to put the legend on. Default is right
legend_fontsize: Font size for legends. Default is 10
anno_fontsize: Font size for annotations. Default is 8
add_borders: whether padding should be added around each box in the comut body.
show_barcodes: whether the sample ids should be shown in the plot
id_order: optional vector with order of Tumor_Sample_Barcodes
ids: optional vector of Tumor_Sample_Barcodes to show
...: variable arguments to pass to Heatmap call

Value

Comut Plot

Examples


input_maf <- data.frame(
 Tumor_Sample_Barcode = c("1", "1", "1", "2", "3", "4", "4"),
 Hugo_Symbol = c("A", "B", "C", "C", "A", "A", "B"),
 Variant_Classification = c(
   "Missense_Mutation", "Nonsense_Mutation",
   "In_Frame_Del", "In_Frame_Del", "Missense_Mutation",
   "Nonsense_Mutation", "Nonsense_Mutation"))

ComutR::comut(data = input_maf)