https://github.com/stemangiola/tidyHeatmap
Draw heatmap simply using a tidy data frame
https://github.com/stemangiola/tidyHeatmap
brewer complexheatmap custom-palette dplyr graphviz heatmap mtcars plotting r rstudio scale tibble tidy tidy-data-frame tidybulk tidyverse viridis
Last synced: 4 months ago
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Draw heatmap simply using a tidy data frame
- Host: GitHub
- URL: https://github.com/stemangiola/tidyHeatmap
- Owner: stemangiola
- Created: 2020-01-13T06:59:37.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2025-07-09T12:09:25.000Z (4 months ago)
- Last Synced: 2025-07-11T04:02:51.868Z (4 months ago)
- Topics: brewer, complexheatmap, custom-palette, dplyr, graphviz, heatmap, mtcars, plotting, r, rstudio, scale, tibble, tidy, tidy-data-frame, tidybulk, tidyverse, viridis
- Language: R
- Homepage: https://stemangiola.github.io/tidyHeatmap/articles/introduction.html
- Size: 62.1 MB
- Stars: 345
- Watchers: 6
- Forks: 25
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
The tidyHeatmap package
================
Stefano Mangiola
2025-01-26
[](https://lifecycle.r-lib.org/articles/stages.html)
[](https://doi.org/10.21105/joss.02472)
`tidyHeatmap` is a package that introduces tidy principles to the
creation of information-rich heatmaps. This package uses
[ComplexHeatmap](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html)
as 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,
Please have a look also to
- [tidygate](https://github.com/stemangiola/tidygate/) for adding custom
gate information to your tibble
- [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/)
for tidy manipulation of Seurat objects
- [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy
manipulation of Seurat objects
- [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy
high-level data analysis and manipulation
- [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/)
for heatmaps produced with tidy principles
## Full documentation [here](https://stemangiola.github.io/tidyHeatmap/articles/introduction.html)
``` r
# 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:
``` r
# 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
``` r
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)
``` r
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 issue
[here](https://github.com/stemangiola/tidyHeatmap/issues)