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Gene barplot

Source: R/oncoplot.R
ggoncoplot_gene_barplot.Rd

Gene barplot

Usage

ggoncoplot_gene_barplot(
  data,
  fontsize_count = 14,
  palette = NULL,
  colour_mutation_type_unspecified = "grey10",
  show_axis,
  total_samples,
  show_genebar_labels = TRUE,
  genebar_label_nudge = 2,
  genebar_label_padding = 0.2,
  only_pad_if_labels_shown = TRUE,
  digits_to_round_to = 0,
  genebar_scale_n_breaks = 3,
  genebar_scale_breaks = ggplot2::waiver()
)

Arguments

data

data frame output by ggoncoplot_prep_df

fontsize_count

fontsize of gene mutation count x axis (number)

palette

a named vector mapping all possible mutation types (vector names) to colors (vector values, optional)

colour_mutation_type_unspecified

colour of mutations in oncoplot and margin plots if col_mutation_type is not supplied (string)

show_axis

show axis text/ticks/line (flag)

total_samples

Strategy for calculating the total number of samples. This value is used to compute the proportion of mutation recurrence displayed in the tooltip when hovering over the gene barplot, or as a text annotation when ggoncoplot_options(show_genebar_labels = TRUE) is set to TRUE.

Possible values:

  • any_mutations: All the samples that are in data (the mutation dataset), irrespective of whether they are on the oncoplot or not.

  • oncoplot: Only the samples that are present on the oncoplot.

  • all: All the samples in either data or metadata.

show_genebar_labels

should gene barplot be labelled with % of samples the gene is mutated in (flag)

genebar_label_nudge

how much padding to add between the gene barplot and bar annotations (number)

genebar_label_padding

how much padding to add to the x axis of the gene barplot (number)

only_pad_if_labels_shown

should expansion to x axis be applied if bar labels aren't shown?

digits_to_round_to

how many digits to round recurrence proportions to

genebar_scale_n_breaks

an integer guiding the number of breaks The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if genebar_scale_breaks = ggplot2::waiver(). Use NULL to use the default

genebar_scale_breaks

fine-grained control over the x axis breaks on the gene barplot. One of:

  • NULL for no minor breaks

  • waiver() for the default breaks (none for discrete, one minor break between each major break for continuous)

  • A numeric vector of positions

  • A function that given the limits returns a vector of minor breaks. When the function has two arguments, it will be given the limits and major break positions.

Value

ggplot showing gene mutation counts