tidyHeatmap

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
group_by	dplyr function - groups heatpmap rows/columns
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_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
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 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
## # ℹ 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"   ) |>
    annotation_tile(hp)

## Warning: Using one column matrices in `filter()` was deprecated in dplyr 1.1.0.
## ℹ Please use one dimensional logical vectors instead.
## ℹ The deprecated feature was likely used in the tidyHeatmap package.
##   Please report the issue at <https://github.com/stemangiola/tidyHeatmap>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

mtcars_heatmap

Saving

mtcars_heatmap |> save_pdf("mtcars_heatmap.pdf")

Clustering

Choose alternative clustering distance and methods.

tidyHeatmap::pasilla |>
    
    heatmap(
        .column = sample,
        .row = symbol,
        .value = `count normalised adjusted`,   
        scale = "row",
        
        # Arguments passed to ComplexHeatmap 
        clustering_distance_rows = "manhattan",
        clustering_distance_columns = "manhattan",
        clustering_method_rows = "ward.D",
        clustering_method_columns = "ward.D"
    ) 

Grouping and splitting

We can easily group the data (one group per dimension maximum, at the moment only the vertical dimension is supported) with dplyr, and the heatmap will be grouped accordingly

# Make up more groupings
mtcars_tidy_groupings = 
    mtcars_tidy |>
    mutate(property_group = if_else(Property %in% c("cyl", "disp"), "Engine", "Other"))

mtcars_tidy_groupings |> 
    group_by(vs, property_group) |>
    heatmap(`Car name`, Property, Value,    scale = "row"   ) |>
    annotation_tile(hp)

We can provide colour palettes to groupings

mtcars_tidy_groupings |> 
    group_by(vs, property_group) |>
    heatmap(
        `Car name`, Property, Value ,   
        scale = "row",
        palette_grouping = list(
            
            # For first grouping (vs)
            c("#66C2A5", "#FC8D62"), 
            
            # For second grouping (property_group)
            c("#b58b4c", "#74a6aa")
        )
    ) |>
    annotation_tile(hp)

We can split based on the cladogram

mtcars_tidy |> 
    heatmap(`Car name`, Property, Value,    scale = "row"   ) |>
    split_rows(2) |>
    split_columns(2)

We can split on kmean clustering (using ComplexHeatmap options, it is stochastic)

mtcars_tidy |> 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row",
        row_km = 2,
        column_km = 2
    ) 

Custom palettes

We can easily use custom palette, using strings, hexadecimal color character vector,

mtcars_tidy |> 
    heatmap(
        `Car name`, 
        Property, 
        Value,  
        scale = "row",
        palette_value = c("red", "white", "blue")
    )

A better-looking blue-to-red palette

mtcars_tidy |> 
    heatmap(
        `Car name`, 
        Property, 
        Value,  
        scale = "row",
        palette_value = circlize::colorRamp2(
            seq(-2, 2, length.out = 11), 
            RColorBrewer::brewer.pal(11, "RdBu")
        )
    )

Or a grid::colorRamp2 function for higher flexibility

mtcars_tidy |> 
    heatmap(
        `Car name`, 
        Property, 
        Value,  
        scale = "row",
        palette_value = circlize::colorRamp2(c(-2, -1, 0, 1, 2), viridis::magma(5))
    )

We can use custom colors for tile annotation

mtcars_tidy |> 
    heatmap(
        `Car name`, 
        Property, 
        Value,  
        scale = "row"
    ) |>
    add_tile(
        hp, 
        palette = c("red", "white", "blue")
    )

## Warning: `add_tile()` was deprecated in tidyHeatmap 1.9.0.
## ℹ Please use `annotation_tile()` instead
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

We can use grid::colorRamp2 function for tile annotation for specific color scales

mtcars_tidy |> 
    heatmap(
        `Car name`, 
        Property, 
        Value,  
        scale = "row"
    ) |>
    annotation_tile(
        hp, 
        palette = circlize::colorRamp2(c(0, 100, 200, 300), viridis::magma(4))
    )

Multiple groupings and annotations

tidyHeatmap::pasilla |>
    group_by(location, type) |>
    heatmap(
        .column = sample,
        .row = symbol,
        .value = `count normalised adjusted`,   
        scale = "row"
    ) |>
    annotation_tile(condition) |>
    annotation_tile(activation)

Remove legends, adding aesthetics to annotations in a modular fashion, using ComplexHeatmap arguments

tidyHeatmap::pasilla |>
    group_by(location, type) |>
    heatmap(
        .column = sample,
        .row = symbol,
        .value = `count normalised adjusted`,   
        scale = "row",
        show_heatmap_legend = FALSE
    ) |>
    annotation_tile(condition, show_legend = FALSE) |>
    annotation_tile(activation, show_legend = FALSE)

Annotation types

“tile”, “point”, “bar” and “line” are available

# Create some more data points
pasilla_plus <- 
    tidyHeatmap::pasilla |>
    dplyr::mutate(act = 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_tile(condition) |>
    annotation_point(activation) |>
    annotation_tile(act) |>
    annotation_bar(size) |>
    annotation_line(age)

Annotation size

We can customise annotation sizes using the grid::unit(), and the size of their names using in-built ComplexHeatmap arguments

pasilla_plus |>
    heatmap(
        .column = sample,
        .row = symbol,
        .value = `count normalised adjusted`,   
        scale = "row"
    ) |>
    annotation_tile(condition, size = unit(0.3, "cm"),  annotation_name_gp= gpar(fontsize = 8)) |>
    annotation_point(activation, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8)) |>
    annotation_tile(act, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8)) |>
    annotation_bar(size, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8)) |>
    annotation_line(age, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8))

Layer symbol

Add a layer on top of the heatmap

tidyHeatmap::pasilla |>
    
    # filter
    filter(symbol %in% head(unique(tidyHeatmap::pasilla$symbol), n = 10)) |>
    
    # Add dynamic size
    mutate(my_size = runif(n(), 1,5)) |> 
    
    heatmap(
        .column = sample,
        .row = symbol,
        .value = `count normalised adjusted`,   
        scale = "row"
    ) |> 
    layer_point(
        `count normalised adjusted log` > 6 & sample == "untreated3"
    ) |>
    layer_square(
        `count normalised adjusted log` > 6 & sample == "untreated2",
        .size = my_size
    ) |>
    layer_arrow_up(
        `count normalised adjusted log` > 6 & sample == "untreated1",
        .size = 4
    )

Layer text

Add a text layer on top of the heatmap

tidyHeatmap::pasilla |>
    
    # filter
    filter(symbol %in% head(unique(tidyHeatmap::pasilla$symbol), n = 10)) |>
    
    # Add dynamic text
    mutate(my_text = "mt", my_size = 7) |> 
    
    # Plot
    heatmap(
        .column = sample,
        .row = symbol,
        .value = `count normalised adjusted`,   
        scale = "row"
    ) |> 
    layer_text(
        `count normalised adjusted log` > 6 & sample == "untreated3", 
        .value = "a", 
        .size = 15
    ) |> 
    layer_text(
    `count normalised adjusted log` > 6 & sample == "untreated2", 
    .value = my_text,
    .size = my_size
)

Adding heatmap side-by-side

p_heatmap = heatmap(mtcars_tidy, `Car name`, Property, Value, scale = "row") 

p_heatmap + p_heatmap

ComplexHeatmap further styling

Add cell borders

mtcars_tidy |> 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row", 
        rect_gp = grid::gpar(col = "#161616", lwd = 0.5)
    ) 

Drop row clustering

mtcars_tidy |> 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row", 
        cluster_rows = FALSE
    ) 

Reorder rows elements

library(forcats)
mtcars_tidy |> 
    mutate(`Car name` = fct_reorder(`Car name`, `Car name`, .desc = TRUE)) %>% 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row", 
        cluster_rows = FALSE
    ) 

Size of dendrograms

mtcars_tidy |> 
    mutate(`Car name` = fct_reorder(`Car name`, `Car name`, .desc = TRUE)) %>% 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row", 
        column_dend_height = unit(0.2, "cm"), 
        row_dend_width = unit(0.2, "cm")
    ) 

Size of rows/columns titles and names

mtcars_tidy |> 
    mutate(`Car name` = fct_reorder(`Car name`, `Car name`, .desc = TRUE)) %>% 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row", 
        row_names_gp = gpar(fontsize = 7),
        column_names_gp = gpar(fontsize = 7),
        column_title_gp = gpar(fontsize = 7),
        row_title_gp = gpar(fontsize = 7)
    ) 

External ComplexHeatmap functionalities

ComplexHeatmap has some graphical functionalities that are not included in the standard functional framework. We can use as_ComplexHeatmap to convert our output before applying drawing options.

Chainging side of legends

heatmap(mtcars_tidy, `Car name`, Property, Value, scale = "row" ) %>%
    as_ComplexHeatmap() %>%
    ComplexHeatmap::draw(heatmap_legend_side = "left"   )

Add title using draw from ComplexHeatmap

mtcars_tidy |> 
    heatmap(`Car name`, Property, Value,    scale = "row"   ) |>
    as_ComplexHeatmap() |>
    ComplexHeatmap::draw(
        column_title = "TITLE", 
        column_title_gp = gpar(fontsize = 16)
    )

Using patchwork to integrate heatmaps

library(ggplot2)
library(patchwork)

p_heatmap =
    mtcars_tidy |> 
    heatmap(
        `Car name`, Property, Value,    
        scale = "row", 
            show_heatmap_legend = FALSE,
        row_names_gp = gpar(fontsize = 7)
    ) 

p_ggplot = data.frame(value = 1:10) |> ggplot(aes(value)) + geom_density()

wrap_heatmap(p_heatmap) + 
    p_ggplot +
    
    # Add padding for better aesthetics
    wrap_heatmap(
        p_heatmap,
        padding = grid::unit(c(-30, -0, -0, -10), "points" ),
        clip = FALSE
    ) + 
    plot_layout(width = c(1, 0.3, 1))

Add title using ggtitle from ggplot2

mtcars_tidy |> 
    heatmap(`Car name`, Property, Value,  scale = "row" ) |>
    wrap_heatmap() +
        ggplot2::ggtitle("TITLE")