heatmap-method: Creates a 'InputHeatmap' object from 'tbl_df' on evaluation...

In stemangiola/tidyHeatmap: A Tidy Implementation of 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 signature 'tbl'
heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  scale = "none",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  .scale = NULL,
  ...
)

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

Arguments

.data	A 'tbl_df' formatted as | <ELEMENT> | <FEATURE> | <VALUE> | <...> |
.row	The name of the column vertically presented in the heatmap
.column	The name of the column horizontally presented in the heatmap
.value	The name of the column for the value of the element/feature pair
transform	A function, used to transform .value row-wise (e.g., transform = log1p)
scale	A character string. Possible values are c(\"none\", \"row\", \"column\", \"both\")
palette_value	A character vector This is the palette that will be used as gradient for .value. For example c("red", "white", "blue"). For higher flexibility you can use circlize::colorRamp2\(c\(-2, -1, 0, 1, 2\), viridis::magma\(5\)\)
palette_grouping	A list of character vectors. This is the list of palettes that will be used for grouping. For example list(RColorBrewer::brewer.pal(8, "Accent")) or list(c("#B3E2CD", "#FDCDAC", "#CBD5E8")) or list(c("black", "red"))
.scale	DEPRECATED. please use scale instead \( with no dot prefix \).
...	The arguments that will be passed to the Heatmap function of ComplexHeatmap backend

Details

\lifecycle

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.

Value

A 'InputHeatmap' objects that gets evaluated to a 'ComplexHeatmap' object

A 'InputHeatmap' object

A 'InputHeatmap' object

A 'InputHeatmap' object

Source

[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)

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`,
  )

stemangiola/tidyHeatmap documentation built on Nov. 2, 2024, 12:54 p.m.