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

Maturing lifecycle

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`, )