Stefano Mangiola 2025-01-26
tidyHeatmap is a package that introduces tidy principles to the creation of information-rich heatmaps. This package uses ComplexHeatmap as graphical engine.
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
Please have a look also to
# 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:
annotation_group, e.g. heatmap(...) |> annotation_group(...)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
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")
If you want to contribute to the software, report issues or problems with the software or seek support please open an issue here
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