ggalign (version 1.0.1)

ggoncoplot: Create an OncoPrint

Description

The ggoncoplot() function generates oncoPrint visualizations that display genetic alterations in a matrix format. This function is especially useful for visualizing complex genomic data, such as mutations, copy number variations, and other genomic alterations in cancer research.

Usage

ggoncoplot(
  data = NULL,
  mapping = aes(),
  ...,
  map_width = NULL,
  map_height = NULL,
  reorder_row = reorder_column,
  reorder_column = TRUE,
  width = NA,
  height = NA,
  filling = waiver(),
  theme = NULL,
  active = NULL
)
# S3 method for default
ggoncoplot(
  data = NULL,
  mapping = aes(),
  ...,
  map_width = NULL,
  map_height = NULL,
  reorder_row = reorder_column,
  reorder_column = TRUE,
  width = NA,
  height = NA,
  filling = waiver(),
  theme = NULL,
  active = NULL
)

Value

A HeatmapLayout object.

Arguments

data

A character matrix which encodes the alterations, you can use ";", ":", ",", or "|" to separate multiple alterations.

mapping

Default list of aesthetic mappings to use for main plot in the layout. If not specified, must be supplied in each layer added to the main plot.

...

Additional arguments passed to fortify_matrix().

map_width, map_height

A named numeric value defines the width/height of each alterations.

reorder_row

A boolean value indicating whether to reorder the rows based on the frequency of alterations. You can set this to FALSE, then add align_order(~rowSums(!is.na(.x)), reverse = TRUE) to achieve the same result. You may also need to set strit = FALSE in align_order() if there are already groups.

reorder_column

A boolean value indicating whether to reorder the columns based on the characteristics of the alterations. You can set this to FALSE, then add align_order2(memo_order) to achieve the same result. You may also need to set strit = FALSE in align_order2() if there are already groups.

width, height

The relative width/height of the main plot, can be a unit object.

filling

Same as ggheatmap(), but only "tile" can be used.

theme

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

active

A active() object that defines the context settings when added to a layout.

Details

ggoncoplot() is a wrapper around the ggheatmap() function, designed to simplify the creation of OncoPrint-style visualizations. The function automatically processes the input character matrix by splitting the encoded alterations (delimited by ";", ":", ",", or "|") into individual genomic events and unnesting the columns for visualization.

Examples

# A simple example from `ComplexHeatmap`
mat <- read.table(textConnection(
    "s1,s2,s3
g1,snv;indel,snv,indel
g2,,snv;indel,snv
g3,snv,,indel;snv"
), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE)

ggoncoplot(mat, map_width = c(snv = 0.5), map_height = c(indel = 0.9)) +
    # Note that guide legends from `geom_tile` and `geom_bar` are different.
    # Although they appear similar, the internal mechanisms won't collapse
    # the guide legends. Therefore, we remove the guide legends from
    # `geom_tile`.
    guides(fill = "none") +
    anno_top(size = 0.5) +
    ggalign() +
    geom_bar(aes(fill = value), data = function(x) {
        subset(x, !is.na(value))
    }) +
    anno_right(size = 0.5) +
    ggalign() +
    geom_bar(aes(fill = value), orientation = "y", data = function(x) {
        subset(x, !is.na(value))
    }) &
    scale_fill_brewer(palette = "Dark2", na.translate = FALSE)