tidyHeatmap (version 1.12.2)

heatmap: Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `ComplexHeatmap`

Description

heatmap() takes a tbl object and easily produces a ComplexHeatmap plot, with integration with tibble and dplyr frameworks.

Usage

heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  scale = "none",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  .scale = NULL,
  ...
)
heatmap_(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  scale = "none",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  .scale = NULL,
  ...
)
# S4 method for tbl
heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  scale = "none",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  .scale = NULL,
  ...
)
# S4 method for tbl_df
heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  scale = "none",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  .scale = NULL,
  ...
)

Value

An `InputHeatmap` object that gets evaluated to a `ComplexHeatmap`

A `InputHeatmap` object

A `InputHeatmap` object

A `InputHeatmap` object

Arguments

.data

A `tbl_df` formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |

.row

The name of the column to use as rows

.column

The name of the column to use as columns

.value

The name of the column to use as values

transform

A function to transform the data (optional)

scale

One of "none", "row", "column", or "both" for scaling

palette_value

A character vector of colors or a function for value colors

palette_grouping

A list of color palettes for grouping annotations

.scale

DEPRECATED: Use scale instead

...

Additional arguments passed to ComplexHeatmap

Details

lifecycle::badge("maturing")

This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.

References

Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for modular heatmap production based on tidy principles." Journal of Open Source Software. doi:10.21105/joss.02472.

Examples

tidyHeatmap::N52 |>
  dplyr::group_by( `Cell type`) |>
  tidyHeatmap::heatmap(
   .row = symbol_ct,
   .column = UBR,
   .value = `read count normalised log`,
  )