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Epi Gantt Chart: Visualize Epidemiological Time Intervals

Source: R/geom_epigantt.R
geom_epigantt.Rd

Creates Epi Gantt charts, which are specialized timeline visualizations used in outbreak investigations to track potential exposure periods and identify transmission patterns. They are particularly useful for:

  • Hospital outbreak investigations to visualize patient movements between wards

  • Identifying potential transmission events by showing when cases were in the same location

  • Visualizing common exposure times using overlapping exposure time intervals

The chart displays time intervals as horizontal bars, typically with one row per case/patient. Different colours can be used to represent different locations (e.g., hospital wards) or exposure types. Additional points or markers can show important events like symptom onset or test dates.

geom_epigantt() will adjust the linewidth depending on the number of cases.

Usage

geom_epigantt(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings. Must include:

  • y: Case/patient identifier

  • xmin: Start date/time of interval

  • xmax: End date/time of interval

  • Optional: colour or fill for different locations/categories

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

stat

A ggplot2 stat. Defaults to "identity".

position

A ggplot2 position. Defaults to "identity".

...

Additional parameters:

  • linewidth: Set width of bars directly, disables auto-scaling if set.

  • lw_scaling_factor: Scaling factor for auto-width calculation. The linewidth is calculated as lw_scaling_factor/number_of_rows (default: 90)

  • lw_min: Minimum auto-scaled line width cutoff (default: 1)

  • lw_max: Maximum auto-scaled line width cutoff (default: 8)

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Value

A ggplot2 geom layer that can be added to a plot

See also

theme_mod_legend_bottom()

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
library(tidyr)
library(ggplot2)

# Transform hospital outbreak line list to long format
linelist_hospital_outbreak |>
  pivot_longer(
    cols = starts_with("ward"),
    names_to = c(".value", "num"),
    names_pattern = "ward_(name|start_of_stay|end_of_stay)_([0-9]+)",
    values_drop_na = TRUE
  ) -> df_stays_long

linelist_hospital_outbreak |>
  pivot_longer(cols = starts_with("pathogen"), values_to = "date") -> df_detections_long

# Create Epi Gantt chart showing ward stays and test dates
ggplot(df_stays_long) +
  geom_epigantt(aes(y = Patient, xmin = start_of_stay, xmax = end_of_stay, color = name)) +
  geom_point(aes(y = Patient, x = date, shape = "Date of pathogen detection"),
    data = df_detections_long
  ) +
  scale_y_discrete_reverse() +
  theme_bw() +
  theme_mod_legend_bottom()
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_point()`).