input_heatmap: input_heatmap

Description

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

Usage

input_heatmap(
  .data,
  .horizontal,
  .vertical,
  .abundance,
  transform = NULL,
  scale = "none",
  palette_value = c("#440154FF", "#21908CFF", "#fefada"),
  palette_grouping = list(),
  ...
)

Value

A `ComplexHeatmap` object

Arguments

.data: A `tbl` formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.horizontal: The name of the column horizontally presented in the heatmap
.vertical: The name of the column vertically presented in the heatmap
.abundance: The name of the transcript/gene abundance column
transform: A function, used to transform .value, for example log1p
scale: A character string. Possible values are c(\"none\", \"row\", \"column\", \"both\")
palette_value: A character vector, or a function for higher customisation (colorRamp2). This is the palette that will be used as gradient for abundance. If palette_value is a vector of hexadecimal colours, it should have 3 values. If you want more customisation, you can pass to palette_value a function, that is derived as for example `colorRamp2(c(-2, 0, 2), palette_value)`
palette_grouping: A list of character vectors. This is the list of palettes that will be used for grouping
...: Further arguments to be passed to ComplexHeatmap::Heatmap

Details

To be added.

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.