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About the developer

stemangiola
148 Stars 11 Forks 253 Commits 8 Opened issues

Description

Draw heatmap simply using a tidy data frame

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tidyHeatmap

Lifecycle:maturing DOI <!-- badges: end -->

Please have a look also to

  • nanny for tidy high-level data analysis and manipulation
  • tidygate for adding custom gate information to your tibble
  • tidySCE for tidy manipulation of Seurat objects
  • tidyseurat for tidy manipulation of Seurat objects
  • tidybulk for tidy high-level data analysis and manipulation
  • tidySE 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
| Plot base heatmap | |
add_tile
| Add tile annotation to the heatmap | |
add_point
| Add point annotation to the heatmap | |
add_bar
| Add bar annotation to the heatmap | |
add_line
| Add line annotation to the heatmap | |
save_pdf
| Save 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 % 
    as_tibble(rownames="Car name") %>% 

# Scale
mutate_at(vars(-`Car name`, -hp, -vs), scale) %&gt;%

# tidyfy
pivot_longer(cols = -c(`Car name`, hp, vs), names_to = "Property", values_to = "Value")

mtcars_tidy

## # A tibble: 288 x 5

Car name hp vs Property Value[,1]

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

Plot

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 % 
        heatmap(`Car name`, Property, Value ) %>%
        add_tile(hp)

mtcars_heatmap

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Save

mtcars_heatmap %>% save_pdf("mtcars_heatmap.pdf")

Grouping

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

mtcars_tidy %>% 
    group_by(vs) %>%
    heatmap(`Car name`, Property, Value ) %>%
    add_tile(hp)

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Custom palettes

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

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

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Or a grid::colorRamp2 function for higher flexibility

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

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Multiple groupings and annotations

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

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Annotation types

This feature requires >= 0.99.20 version

“tile” (default), “point”, “bar” and “line” are available

# Create some more data points
pasilla_plus %
        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 ) %>% add_tile(condition) %>% add_point(activation) %>% add_tile(act) %>% add_bar(size) %>% add_line(age)

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