GitHub - stemangiola/tidyHeatmap: Draw heatmap simply using a tidy data frame (original) (raw)
The tidyHeatmap package
Stefano Mangiola 2025-01-26
tidyHeatmap is a package that introduces tidy principles to the creation of information-rich heatmaps. This package usesComplexHeatmapas graphical engine.
Citation
Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap production based on tidy principles. Journal of Open Source Software, 5(52), 2472, https://doi.org/10.21105/joss.02472
Full documentation here
Create some more data points
pasilla_plus <- tidyHeatmap::pasilla |> dplyr::mutate(activation_2 = activation, activation_3 = activation) |> tidyr::nest(data = -sample) |> dplyr::mutate(size = rnorm(n(), 4,0.5)) |> dplyr::mutate(age = runif(n(), 50, 200)) |> tidyr::unnest(data)
Plot
pasilla_plus |>
heatmap(
.column = sample,
.row = symbol,
.value = count normalised adjusted,
scale = "row"
) |>
annotation_group(location) |>
annotation_tile(condition, show_legend = FALSE) |>
annotation_point(activation) |>
annotation_numeric(activation_3) |>
annotation_tile(activation_2) |>
annotation_bar(size) |>
annotation_line(age)
Advantages:
- Modular annotation with just specifying column names
- Custom grouping of rows/columns is easy to specify with
annotation_group, e.g.heatmap(...) |> annotation_group(...) - Labels size adjusted by row and column total number
- Default use of Brewer and Viridis palettes
Retrieve heatmap data and dendrograms
After creating a heatmap, you can extract the matrix and dendrograms exactly as they appear in the plot:
Create heatmap
hm <- tidyHeatmap::N52 |>
tidyHeatmap::heatmap(
.row = symbol_ct,
.column = UBR,
.value = read count normalised log
)
Extract heatmap data as plotted
result <- hm |> get_heatmap_data() ordered_matrix <- result$matrix # Matrix with rows/columns in heatmap order row_dendrogram <- result$row_dend # Row dendrogram object column_dendrogram <- result$column_dend # Column dendrogram object
All have consistent row and column names
print(rownames(ordered_matrix)) print(labels(row_dendrogram))
Functions/utilities available
| Function | Description |
|---|---|
| heatmap | Plots base heatmap |
| annotation_group | Adds group annotation strips and grouping to the heatmap |
| annotation_tile | Adds tile annotation to the heatmap |
| annotation_point | Adds point annotation to the heatmap |
| annotation_bar | Adds bar annotation to the heatmap |
| annotation_numeric | Adds bar + number annotation to the heatmap |
| annotation_line | Adds line annotation to the heatmap |
| layer_text | Add layer of text on top of the heatmap |
| layer_point | Adds layer of symbols on top of the heatmap |
| layer_square | Adds layer of symbols on top of the heatmap |
| layer_diamond | Adds layer of symbols on top of the heatmap |
| layer_arrow_up | Adds layer of symbols on top of the heatmap |
| layer_arrow_down | Add layer of symbols on top of the heatmap |
| layer_star | Add layer of symbols on top of the heatmap |
| layer_asterisk | Add layer of symbols on top of the heatmap |
| split_rows | Splits the rows based on the dendogram |
| split_columns | Splits the columns based on the dendogram |
| get_heatmap_data | Retrieves matrix and dendrograms exactly as plotted |
| save_pdf | Saves the PDF of the heatmap |
| + | Integrate heatmaps side-by-side |
| as_ComplexHeatmap | Convert the tidyHeatmap output to ComplexHeatmap for non-standard "drawing" |
| wrap_heatmap | Allows the integration with the patchwork package |
Installation
To install the most up-to-date version
devtools::install_github("stemangiola/tidyHeatmap")
To install the most stable version (however please keep in mind that this package is under a maturing lifecycle stage)
install.packages("tidyHeatmap")
Contribution
If you want to contribute to the software, report issues or problems with the software or seek support please open an issuehere