Extended: More Complex Pedigree Plots with ggPedigreeInteractive

library(ggpedigree) # ggPedigree lives here
library(BGmisc) # helper utilities & example data
library(ggplot2) # ggplot2 for plotting
library(viridis) # viridis for color palettes
library(tidyverse) # for data wrangling

This vignette demonstrates how to create interactive pedigree plots using the ggPedigreeInteractive() function from the ggpedigree package. It extends the basic examples found in the main package documentation.

Customising labels and tool‑tips

ggPedigreeInteractive() accepts the same config list as ggPedigree(), plus the tooltip_columns 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,
    label_include = TRUE,
    label_method = "geom_text",
    sex_color_include = TRUE
  ),
  tooltip_columns = 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,
    label_include = TRUE,
    label_method = "geom_text",
    sex_color_include = TRUE,
    return_static = TRUE
  ),
  tooltip_columns = 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(
    option = "inferno",
    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

Customizing the interactive plot

You can customize the interactive plot further by modifying the layout, adding titles, and adjusting hover labels. The plotly::layout() function allows you to set various layout options such as title, margins, and hover label styles.

library(BGmisc)
data(hazard)

df <- hazard

ggPedigreeInteractive(
  df,
  famID = "famID",
  personID = "ID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    code_male = 0,
    status_column = "affected",
    label_nudge_y = .25,
    label_include = TRUE,
    include_tooltip = TRUE,
    label_method = "geom_text",
    sex_color_include = TRUE
  ),
  tooltip_columns = c("personID", "birthYr", "onsetYr", "deathYr")
) %>%
  plotly::layout(
    title = "Hazard Pedigree (interactive)",
    hoverlabel = list(bgcolor = "white"),
    margin = list(l = 50, r = 50, t = 50, b = 50)
  ) %>%
  plotly::config(displayModeBar = TRUE)
#> Warning in buildPlotConfig(default_config = default_config, config = config, :
#> The following config values are not recognized by getDefaultPlotConfig():
#> include_tooltip

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.