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Interactive Pedigree Plotting with ggPedigreeInteractive()

Introduction

The ggPedigreeInteractive() function extends the static pedigree plots generated by ggPedigree() into fully interactive Plotly widgets. This allows users to explore pedigree data in a more dynamic way, with features such as hover text, zooming, and panning. This vignette walks through: - Basic usage of ggPedigreeInteractive() - Customizing the interactive plot - Adding tooltips for additional information

# Load required packages
library(BGmisc) # ships the sample 'potter' pedigree
library(ggplot2) # used internally by ggPedigree*
library(viridis) # viridis for color palettes
library(plotly) # conversion layer for interactivity
#> 
#> Attaching package: 'plotly'
#> The following object is masked from 'package:ggplot2':
#> 
#>     last_plot
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> The following object is masked from 'package:graphics':
#> 
#>     layout
library(ggpedigree) # the package itself

Example data

The package includes a small toy pedigree for the Harry Potter universe:

# Load the example data
data("potter")
# Display the first few rows of the dataset
head(potter)
#>   personID famID             name gen momID dadID spouseID sex
#> 1        1     1   Vernon Dursley   1   101   102        3   1
#> 2        2     1 Marjorie Dursley   1   101   102       NA   0
#> 3        3     1    Petunia Evans   1   103   104        1   0
#> 4        4     1       Lily Evans   1   103   104        5   0
#> 5        5     1     James Potter   1    NA    NA        4   1
#> 6        6     1   Dudley Dursley   2     3     1       NA   1

Basic Usage

A minimal call is just:

ggPedigreeInteractive(potter)

…but you will usually want to identify the core primary‑key columns in advance:

plt <- ggPedigreeInteractive(
  potter,
  famID    = "famID",
  personID = "personID",
  momID    = "momID",
  dadID    = "dadID"
) |> plotly::hide_legend()

plt

Customising labels and tool‑tips

ggPedigreeInteractive() accepts the same config list as ggPedigree(), plus the tooltip_cols argument for hover text. Below we enable node labels, nudge them upward a little, color by sex, and show both the personID and name fields in the hover:

plt <- ggPedigreeInteractive(
  potter,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    label_nudge_y   = -.25,
    include_labels  = TRUE,
    label_method    = "geom_text",
    sex_color       = TRUE
  ),
  tooltip_cols = c("personID", "name")
)

plt

Further customisation

Adding tooltips

Because the function returns a Plotly object, you can layer additional modifications on top:

plt2 <- plt %>%
  plotly::layout(
    title = "The Potter Family Tree (interactive)",
    hoverlabel = list(bgcolor = "white"),
    margin = list(l = 50, r = 50, t = 50, b = 50)
  ) %>%
  plotly::config(displayModeBar = TRUE)

plt2

You can also save the widget as standalone HTML:

htmlwidgets::saveWidget(
  plt,
  file = "potter_interactive.html",
  selfcontained = TRUE
)
# Note: The above code will save the widget in the current working directory.

Static Plot customisation

You can also create a static version of the plot using the return_static argument. This is useful for generating high-quality images for reports or publications. The static plot can be further customized using ggplot2 functions. It can also be plotted using plotly::ggplotly() to retain interactivity.

static <- ggPedigreeInteractive(
  potter,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    label_nudge_y = -.25,
    include_labels = TRUE,
    label_method = "geom_text",
    sex_color = TRUE,
    return_static = TRUE
  ),
  tooltip_cols = c("personID", "name")
)

The static plot can be further customized using ggplot2 functions.

static_plot <- static +
  ggplot2::labs(
    title = "The Potter Family Tree (static)",
    subtitle = "This is a static plot"
  ) +
  theme_bw(base_size = 12) +
  theme(
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line        = element_line(colour = "black"),
    axis.text.x      = element_blank(),
    axis.text.y      = element_blank(),
    axis.ticks.x     = element_blank(),
    axis.ticks.y     = element_blank(),
    axis.title.x     = element_blank(),
    axis.title.y     = element_blank()
  ) + scale_color_viridis(
    discrete = TRUE,
    labels = c("Female", "Male", "Unknown")
  )
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.

static_plot

You can also convert the static plot back to an interactive plot using plotly::ggplotly():

plt2 <- plotly::ggplotly(static_plot,
  tooltip = "text",
  width   = NULL,
  height  = NULL
)

plt2

Conclusion

ggPedigreeInteractive() provides a powerful way to visualize pedigree data interactively. By leveraging the capabilities of Plotly, users can explore their data in a more dynamic and engaging manner. The function is designed to be flexible, allowing for customization of labels, tooltips, and overall aesthetics.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.