Overview of the tidyHeatmap package

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

Please have a look also to

tidygate for adding custom gate information to your tibble
tidySingleCellExperiment for tidy manipulation of Seurat objects
tidyseurat for tidy manipulation of Seurat objects
tidybulk for tidy high-level data analysis and manipulation
tidySummarizedExperiment for heatmaps produced with tidy principles

website: stemangiola.github.io/tidyHeatmap

tidyHeatmap is a package that introduces tidy principles to the creation of information-rich heatmaps. This package uses ComplexHeatmap as graphical engine.

Advantages:

Modular annotation with just specifying column names
Custom grouping of rows is easy to specify providing a grouped tbl. For example df |> group_by(...)
Labels size adjusted by row and column total number
Default use of Brewer and Viridis palettes

Functions/utilities available

Function	Description
`heatmap`	Plots base heatmap
`add_tile`	Adds tile annotation to the heatmap
`add_point`	Adds point annotation to the heatmap
`add_bar`	Adds bar annotation to the heatmap
`add_line`	Adds line annotation to 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
`split_rows`	Splits the rows based on the dendogram
`split_columns`	Splits the columns based on the dendogram
`save_pdf`	Saves the PDF of the heatmap

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 issue here

Input data frame

The heatmaps visualise a multi-element, multi-feature dataset, annotated with independent variables. Each observation is a element-feature pair (e.g., person-physical characteristics).

element	feature	value	independent_variables
`chr` or `fctr`	`chr` or `fctr`	`numeric`	…

Let’s transform the mtcars dataset into a tidy “element-feature-independent variables” data frame. Where the independent variables in this case are ‘hp’ and ‘vs’.

mtcars_tidy <- 
    mtcars |> 
    as_tibble(rownames="Car name") |> 
    
    # Scale
    mutate_at(vars(-`Car name`, -hp, -vs), scale) |>
    
    # tidyfy
    pivot_longer(cols = -c(`Car name`, hp, vs), names_to = "Property", values_to = "Value")

mtcars_tidy

## # A tibble: 288 × 5
##    `Car name`       hp    vs Property Value[,1]
##    <chr>         <dbl> <dbl> <chr>        <dbl>
##  1 Mazda RX4       110     0 mpg          0.151
##  2 Mazda RX4       110     0 cyl         -0.105
##  3 Mazda RX4       110     0 disp        -0.571
##  4 Mazda RX4       110     0 drat         0.568
##  5 Mazda RX4       110     0 wt          -0.610
##  6 Mazda RX4       110     0 qsec        -0.777
##  7 Mazda RX4       110     0 am           1.19 
##  8 Mazda RX4       110     0 gear         0.424
##  9 Mazda RX4       110     0 carb         0.735
## 10 Mazda RX4 Wag   110     0 mpg          0.151
## # … with 278 more rows

Plotting

For plotting, you simply pipe the input data frame into heatmap, specifying:

The rows, cols relative column names (mandatory)
The value column name (mandatory)
The annotations column name(s)

mtcars

mtcars_heatmap <- 
    mtcars_tidy |> 
    heatmap(`Car name`, Property, Value,    scale = "row"   ) |>
    add_tile(hp)

mtcars_heatmap