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

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

heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  .scale = "row",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  annotation = NULL,
  type = rep("tile", length(quo_names(annotation))),
  palette_discrete = list(),
  palette_continuous = list(),
  .abundance = NULL,
  .horizontal = NULL,
  .vertical = NULL,
  log_transform = NULL,
  palette_abundance = NULL,
  ...
)

heatmap_(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  .scale = "row",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  annotation = NULL,
  type = rep("tile", length(quo_names(annotation))),
  palette_discrete = list(),
  palette_continuous = list(),
  .abundance = NULL,
  .horizontal = NULL,
  .vertical = NULL,
  log_transform = NULL,
  palette_abundance = NULL,
  ...
)

# S4 method for tbl
heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  .scale = "row",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  annotation = NULL,
  type = rep("tile", length(quo_names(annotation))),
  palette_discrete = list(),
  palette_continuous = list(),
  .abundance = NULL,
  .horizontal = NULL,
  .vertical = NULL,
  log_transform = NULL,
  palette_abundance = NULL,
  ...
)

# S4 method for tbl_df
heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  .scale = "row",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  annotation = NULL,
  type = rep("tile", length(quo_names(annotation))),
  palette_discrete = list(),
  palette_continuous = list(),
  .abundance = NULL,
  .horizontal = NULL,
  .vertical = NULL,
  log_transform = NULL,
  palette_abundance = NULL,
  ...
)

# S4 method for tidybulk
heatmap(
  .data,
  .row,
  .column,
  .value,
  transform = NULL,
  .scale = "row",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  annotation = NULL,
  type = rep("tile", length(quo_names(annotation))),
  palette_discrete = list(),
  palette_continuous = list(),
  .abundance = NULL,
  .horizontal = NULL,
  .vertical = NULL,
  log_transform = NULL,
  palette_abundance = 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 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
annotation	DEPRECATED. please use the annotation functions add_* function \(\* one of tile, point, bar, line \).
type	DEPRECATED. please use the annotation functions add_* function \(\* one of tile, point, bar, line \).
palette_discrete	DEPRECATED. please use the annotation functions add_* function \(\* one of tile, point, bar, line \).
palette_continuous	DEPRECATED. please use the annotation functions add_* function \(\* one of tile, point, bar, line \).
.abundance	DEPRECATED. Please use .value instead
.horizontal	DEPRECATED. Please use .column instead
.vertical	DEPRECATED. Please use .row instead
log_transform	DEPRECATED. Please use transform instead
palette_abundance	DEPRECATED. Please use palette_value instead
...	Further arguments to be passed to ComplexHeatmap::Heatmap

Value

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

A `InputHeatmap` object

A `InputHeatmap` object

A `InputHeatmap` object

A `InputHeatmap` object

Details

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.

Examples

library(dplyr)

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