ggdiceplot

Fully ggplot compatible implementation for the diceplot plotting library

https://github.com/maflot/ggdiceplot

Repository

Fully ggplot compatible implementation for the diceplot plotting library

README.html

ggdiceplot
A ggplot2 extension for creating dice plot visualizations, where each
dice represents multiple categorical variables using the traditional
dice dot patterns.

Installation
# Install from local directory
devtools::install_local("path/to/ggdiceplot")

# Or install dependencies manually
install.packages(c("ggplot2", "tibble"))


Example 1
library(ggplot2)
library(ggdiceplot)

# Create sample data
toy_data1 <- data(sample_dice_data1)

# Effect size
lo = floor(min(toy_data$lfc, na.rm = TRUE))
up = ceiling(max(toy_data$lfc, na.rm=TRUE))
mid = (lo + up)/2

minsize = floor(min(-log10(toy_data$q), na.rm=TRUE))
maxsize = ceiling(max(-log10(toy_data$q), na.rm=TRUE))
midsize = ceiling(quantile(-log10(toy_data$q), c(0.5), na.rm=TRUE))

#
## PLOT
#

ggplot(toy_data1, aes(x=specimen, y=taxon)) +
  geom_dice(aes(dots=disease, fill=lfc, size=-log10(q), 
                # Square dims
                width = 0.5, height = 0.5),
            # For legend display
            show.legend=TRUE, 
            # For legend position calculation
            ndots=length(unique(toy_data$disease)),
            # For aspect.ratio: ensure squares
            x_length = length(unique(toy_data$specimen)), 
            y_length = length(unique(toy_data$taxon)), 
            )+
  scale_fill_continuous(name="lfc") +
  scale_fill_gradient2(low = "#40004B", high = "#00441B", mid = "white",
                        na.value = "white", 
                       limit = c(lo, up),
                       midpoint = mid, 
                        name = "Log2FC") +
  scale_size_continuous(limits = c(minsize, maxsize),
                        breaks = c(minsize, midsize, maxsize),
                        labels = c(10^minsize, 10^-midsize, 10^-maxsize),
                        name = "q-value")



Example 2
library(ggplot2)
library(ggdiceplot)

toy_data <- data(sample_dice_data2)

#
## PARAMS
#

# Effect size
lo = floor(min(toy_data$lfc, na.rm = TRUE))
up = ceiling(max(toy_data$lfc, na.rm=TRUE))
mid = (lo + up)/2

minsize = floor(min(-log10(toy_data$q), na.rm=TRUE))
maxsize = ceiling(max(-log10(toy_data$q), na.rm=TRUE))
midsize = ceiling(quantile(-log10(toy_data$q), c(0.5), na.rm=TRUE))

#
## PLOT
#

ggplot(toy_data, aes(x=specimen, y=taxon)) +
  geom_dice(aes(dots=disease, fill=lfc, size=-log10(q), 
                # Square dims
                width = 0.5, height = 0.5),
            # For missing info
            na.rm = TRUE,
            # For legend display
            show.legend=TRUE, 
            # For legend position calculation
            ndots=length(unique(toy_data$disease)),
            # For aspect.ratio: ensure squares
            x_length = length(unique(toy_data$specimen)), 
            y_length = length(unique(toy_data$taxon)), 
  )+
  scale_fill_continuous(name="lfc") +
  scale_fill_gradient2(low = "#40004B", high = "#00441B", mid = "white",
                       na.value = "white", 
                       limit = c(lo, up),
                       midpoint = mid, 
                       name = "Log2FC") +
  scale_size_continuous(limits = c(minsize, maxsize),
                        breaks = c(minsize, midsize, maxsize),
                        labels = c(10^minsize, 10^-midsize, 10^-maxsize),
                        name = "q-value")



Features

Automatic Sizing: Dice automatically scale based on
grid density
Boundary Safety: Dice stay within plot
boundaries
Flexible Mapping: Map any categories to dice
positions 1-6
Multiple Applications: Gene expression, survey
data, clinical trials, market research
Customizable: Control dice size, colors, and
positioning



Key Functions

geom_dice(): Main geom for creating dice plots
create_dice_positions(): Generate standard dice dot
positions



Demo Examples
See the demo_output/ directory for: - Basic
functionality examples - Real-world usage scenarios - Boundary
validation tests - Custom sizing demonstrations
Run the demo scripts:
cd demo_output
Rscript create_demo_plots.R
Rscript usage_examples.R


Package Structure

R/: Core package functions
data/: Sample datasets
demo_output/: Example plots and scripts
inst/examples/: Installation examples
man/: Documentation files
tests/: Unit tests
vignettes/: Extended documentation



Documentation

Package functions: help(package = "ggdiceplot")
Main function: ?geom_dice
Vignette:
vignette("introduction", package = "ggdiceplot")



Citation
If you use this code or the R and Python packages for your own work,
please cite diceplot as:

M. Flotho, P. Flotho, A. Keller, “Diceplot: A package for high
dimensional categorical data visualization,” arxiv, 2024. doi:10.48550/arXiv.2410.23897

BibTeX entry:
@article{flotea2024,
    author = {Flotho, M. and Flotho, P. and Keller, A.},
    title = {Diceplot: A package for high dimensional categorical data visualization},
    year = {2024},
    journal = {arXiv preprint},
    doi = {https://doi.org/10.48550/arXiv.2410.23897}
}


License
This package is licensed under LICENSE.

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