Show mutations in particular genes

Usage

plot_mutations(object, ...)

# S3 method for cevodata
plot_mutations(
  object,
  genes = NULL,
  drivers = NULL,
  mark_genes = NULL,
  y = "genes",
  shape = "impact",
  filter_fun = guess_filter_fun(shape),
  ...
)

# S3 method for tbl_df
plot_mutations(
  object,
  genes = NULL,
  drivers = NULL,
  mark_genes = NULL,
  y = "genes",
  shape = "impact",
  filter_fun = guess_filter_fun(shape),
  ...
)

layer_mutations(
  object,
  mapping = NULL,
  genes = NULL,
  drivers = NULL,
  show_labels = TRUE,
  color = "black",
  size = 3,
  shape = "impact",
  filter_fun = guess_filter_fun(shape),
  ...
)

Arguments

object: cevodata
...: other arguments passed to geom_point()
genes: list of genes for which mutations should be shown
drivers: cancer type, for which mutations in driver genes should be shown. Needs to be taken from driver_genes
mark_genes: list of genes to mark
y: which to show on y axis: "genes" or "samples"
shape: "impact" or "variant_classification"?
filter_fun: Function for filtering mutations: variant_classification_filter() or impact_filter()
mapping: aes()
show_labels: lgl use ggrepel to label the mutations?
color: color
size: size

Value

ggplot obj

Functions

layer_mutations(): Adds mutations to SFS plots