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ggoncoplot options

Source: R/oncoplot.R
ggoncoplot_options.Rd

Customise the look of your oncoplot.

Usage

ggoncoplot_options(
  interactive_svg_width = 12,
  interactive_svg_height = 6,
  selection_type = c("none", "multiple", "single"),
  plotsize_tmb_rel_height = 10,
  plotsize_gene_rel_width = 20,
  plotsize_metadata_rel_height = 20,
  xlab_title = "Sample",
  ylab_title = "Gene",
  fontsize_xlab = 26,
  fontsize_ylab = 26,
  fontsize_genes = 16,
  fontsize_samples = 12,
  fontsize_count = 14,
  fontsize_tmb_title = 14,
  fontsize_tmb_axis = 11,
  fontsize_pathway = 16,
  fontsize_legend_title = 12,
  fontsize_legend_text = 12,
  tile_height = 1,
  tile_width = 1,
  colour_backround = "grey90",
  colour_mutation_type_unspecified = "grey10",
  show_sample_ids = FALSE,
  show_ylab_title = FALSE,
  show_xlab_title = FALSE,
  show_ylab_title_tmb = FALSE,
  show_legend = TRUE,
  show_legend_titles = TRUE,
  show_axis_gene = TRUE,
  show_genebar_labels = FALSE,
  show_axis_tmb = TRUE,
  log10_transform_tmb = TRUE,
  scientific_tmb = FALSE,
  genebar_label_padding = 0.3,
  genebar_only_pad_when_labels_shown = TRUE,
  genebar_label_nudge = 2,
  genebar_label_round = 0,
  genebar_scale_breaks = ggplot2::waiver(),
  genebar_scale_n_breaks = 3,
  colour_pathway_text = "white",
  colour_pathway_bg = "grey10",
  colour_pathway_outline = "black",
  pathway_text_angle = 0,
  ggoncoplot_guide_ncol = 2,
  legend_key_size = 0.4,
  fontsize_metadata_text = 12,
  fontsize_metadata_legend_title = fontsize_legend_title,
  fontsize_metadata_legend_text = fontsize_legend_text,
  fontsize_metadata_barplot_y_numbers = 8,
  metadata_legend_nrow = NULL,
  metadata_legend_ncol = NULL,
  metadata_legend_key_size = legend_key_size,
  metadata_na_marker = "!",
  metadata_na_marker_size = 8,
  metadata_maxlevels = 6,
  metadata_numeric_plot_type = c("bar", "heatmap"),
  metadata_legend_orientation_heatmap = c("horizontal", "vertical")
)

Arguments

interactive_svg_width

dimensions of interactive plot (number)

interactive_svg_height

dimensions of interactive plot (number)

selection_type

Defines the type of data point selection allowed when the ggplot is interactive. Options include 'none' (default), 'multiple' (enables lasso-select tool), and 'single' (supports single-click selection).

plotsize_tmb_rel_height

percentage of vertical space TMB margin plot should take up. Must be some value between 5-90 (number)

plotsize_gene_rel_width

percentage of horizontal space the gene barplot should take up. Must be some value between 5-90 (number)

plotsize_metadata_rel_height

percentage of vertical space the metadata tile plot should take up. Must be some value between 5-90 (number)

xlab_title

x axis label. Set xlab_title = NULL to remove title (string)

ylab_title

y axis of interactive plot. Set ylab_title = NULL to remove title (string)

fontsize_xlab

size of x axis title (number)

fontsize_ylab

size of y axis title (number)

fontsize_genes

size of y axis text (gene names) (number)

fontsize_samples

size of x axis text (sample names). Ignored unless show_sample_ids is set to true (number)

fontsize_count

fontsize of gene mutation count x axis (number)

fontsize_tmb_title

fontsize of y axis title for TMB marginal plot (number)

fontsize_tmb_axis

fontsize of y axis text for TMB marginal plot (number)

fontsize_pathway

fontsize of y axis strip text describing gene pathways (number)

fontsize_legend_title

fontsize of the legend titles (number)

fontsize_legend_text

fontsize of the legend text (number)

tile_height

proportion of available vertical space each tile will take up (0-1) (number)

tile_width

proportion of available horizontal space each tile take up (0-1) (number)

colour_backround

colour used for background non-mutated tiles (string)

colour_mutation_type_unspecified

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

show_sample_ids

show sample_ids_on_x_axis (flag)

show_ylab_title

show y axis title of oncoplot (flag)

show_xlab_title

show x axis title of oncoplot (flag)

show_ylab_title_tmb

show y axis title of TMB margin plot (flag)

show_legend

show the oncoplot legend

show_legend_titles

show legend titles (flag)

show_axis_gene

show x axis line/ticks/labels for gene barplot (flag)

show_genebar_labels

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

show_axis_tmb

show y axis line/ticks/labels for TMB barplot (flag)

log10_transform_tmb

log10 transform total number of mutations for TMB marginal plot (flag)

scientific_tmb

display tmb counts in scientific notation (flag)

genebar_label_padding

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

genebar_only_pad_when_labels_shown

only apply genebar_label_padding when labels are shown (flag)

genebar_label_nudge

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

genebar_label_round

how many digits to round the genebar labels to (number)

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.

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

colour_pathway_text

colour of text describing pathways (string)

colour_pathway_bg

background fill colour of pathway strips (string)

colour_pathway_outline

outline colour of pathway strips (string)

pathway_text_angle

angle of pathway text label (typically 0 or 90 degrees) (number)

ggoncoplot_guide_ncol

how many columns to use when describing oncoplot legend (number)

legend_key_size

width of the legend key block (number)

fontsize_metadata_text

fontsize of the y axis text for in the sample metadata plot (number)

fontsize_metadata_legend_title

fontsize of the titles of metadata legends. Will default to fontsize_legend_text (number)

fontsize_metadata_legend_text

fontsize of the text in metadata legends. Will default to fontsize_legend_title (number)

fontsize_metadata_barplot_y_numbers

fontsize of the text describing numeric barplot max & min values (number)

metadata_legend_nrow

number of rows allowed per metadata legend (number)

metadata_legend_ncol

number of columns allowed per metadata legend (number)

metadata_legend_key_size

width of the legend key block (number). Defaults to legend_key_size

metadata_na_marker

character used to indicate data is missing (string)

metadata_na_marker_size

size of character used when data is missing (number)

metadata_maxlevels

or categorical variables, what is the maximum number of distinct values to allow (too many will make it hard to find a palette that suits) (number)

metadata_numeric_plot_type

visual representation of numeric properties. One of 'bar', for bar charts, or 'heatmap' for heatmaps

metadata_legend_orientation_heatmap

the orientation of heatmaps in legends. One of "horizontal" or "vertical" number of breaks given by the transformation.

Value

ggoncoplot options object ready to be passed to ggoncoplot() options argument

Examples


# Read GBM MAF file
gbm_csv <- system.file(
  package = "ggoncoplot",
  "testdata/GBM_tcgamutations_mc3_maf.csv.gz"
)
gbm_df <- read.csv(file = gbm_csv, header = TRUE)

# Plot Oncoplot and Customise Options
gbm_df |>
  ggoncoplot(
    col_genes = 'Hugo_Symbol',
    col_samples = 'Tumor_Sample_Barcode',
    col_mutation_type = 'Variant_Classification',

    # Customise Visual Options
    options = ggoncoplot_options(

      # Interactive Plot Options
      interactive_svg_width = 12,
      interactive_svg_height = 6,

      # Relative height of different plotsizes
      plotsize_tmb_rel_height = 10,
      plotsize_gene_rel_width = 20,
      plotsize_metadata_rel_height = 20,

      # Axis Titles
      xlab_title = "Glioblastoma Samples",
      ylab_title = "Top 10 mutated genes",

      # Fontsizes
      fontsize_xlab = 40,
      fontsize_ylab = 40,
      fontsize_genes = 16,
      fontsize_samples = 12,
      fontsize_count = 14,
      fontsize_tmb_title = 14,
      fontsize_tmb_axis = 11,
      fontsize_pathway = 16,

      # Customise Tiles
      tile_height = 1,
      tile_width = 1,
      colour_backround = "grey90",
      colour_mutation_type_unspecified = "grey10",

      # Show different elements
      show_sample_ids = FALSE,
      show_ylab_title = FALSE,
      show_xlab_title = FALSE,
      show_ylab_title_tmb = FALSE,
      show_axis_gene = TRUE,
      show_axis_tmb = TRUE,

      # Transformation and label scales
      log10_transform_tmb = TRUE,
      scientific_tmb = FALSE,

      # Gene Barplot Specific Options
      show_genebar_labels = TRUE,
      genebar_label_padding = 0.2,
      genebar_only_pad_when_labels_shown = TRUE,
      genebar_label_nudge = 2,
      genebar_label_round = 1,

      # Pathway Faceting Colours / Text
      colour_pathway_text = "white",
      colour_pathway_bg = "grey10",
      colour_pathway_outline = "black",
      pathway_text_angle = 0,

      # Legend number of columns
      ggoncoplot_guide_ncol = 2
    )
  )
#> 
#> ── Identify Class ──
#> 
#> ℹ Found 7 unique mutation types in input set
#> ℹ 0/7 mutation types were valid PAVE terms
#> ℹ 0/7 mutation types were valid SO terms
#> ℹ 7/7 mutation types were valid MAF terms
#> ✔ Mutation Types are described using valid MAF terms ... using MAF palete