Creates publication-ready plots from objects returned by `compute_eci()` and `compute_ecilag()`. Either object may be supplied alone. When both are supplied, the overall ECI perspective and the lag-specific perspective are combined and labelled "(a)" and "(b)", respectively.
Usage
plot_eci(
eci_overall = NULL,
eci_lag = NULL,
overall_col = c("ECI_weighted", "ECI_raw", "ECI_raw_centered"),
lag_col = c("ECI_weighted", "ECI_percent", "ECI_absolute"),
facet_scales = c("free_y", "fixed", "free", "free_x"),
overall_nrow = 3L,
lag_ncol = 1L,
sample_smooth = TRUE,
smooth_method = NULL,
smooth_formula = NULL,
linewidth = 0.7,
alpha = 0.2,
overall_x_label = "ECI",
overall_y_label = "Predicted",
lag_x_label = "Lag",
lag_y_label = "ECI",
exposure_y_label = "Exposure difference",
exposure_colors = c("#4C72B0", "#C44E52", "#55A868"),
base_size = 10,
panel_labels = c("(a)", "(b)"),
label_size = 12,
rel_widths = NULL
)Arguments
- eci_overall
Optional data frame returned by `compute_eci()`.
- eci_lag
Optional object returned by `compute_ecilag()`. A list with `by_lag_samples` and/or `by_lag` is handled internally. A lag-level data frame is also accepted.
- overall_col
Character scalar selecting the `compute_eci()` column used on the x-axis. One of `"ECI_weighted"`, `"ECI_raw"`, or `"ECI_raw_centered"`. Default is `"ECI_weighted"`.
- lag_col
Character scalar selecting the lag-specific ECI column from `compute_ecilag()` used on the y-axis. One of `"ECI_weighted"`, `"ECI_percent"`, or `"ECI_absolute"`. Default is `"ECI_weighted"`.
- facet_scales
Character scalar controlling facet scales. One of `"fixed"`, `"free"`, `"free_x"`, or `"free_y"`. Default is `"free_y"`.
- overall_nrow
Positive integer number of facet rows for the overall ECI panel. Default is `3`.
- lag_ncol
Positive integer number of facet columns for lag panels. Default is `1`.
- sample_smooth
Logical scalar. If `TRUE`, draw-level curves are shown with `geom_smooth(se = FALSE)`, reproducing the original manual plot. If `FALSE`, draw-level curves are connected with `geom_line()`. Summary outputs are always displayed with a smoothed central curve and, when available, dashed smoothed lower and upper interval curves.
- smooth_method
Optional smoothing method passed to `geom_smooth()`. The default `NULL` lets ggplot2 select its standard method.
- smooth_formula
Optional formula passed to `geom_smooth()`. Default is `NULL`.
- linewidth
Positive finite line width. Default is `0.7`.
- alpha
Finite number in `[0, 1]` retained for backward compatibility with earlier ribbon-based summary plots. Summary uncertainty is now represented by dashed smoothed interval curves. Default is `0.20`.
- overall_x_label, overall_y_label, lag_x_label, lag_y_label,
exposure_y_label Axis labels.
- exposure_y_label
Optional character string defining the y-axis label used for the exposure panel. If `NULL`, a default label is generated.
- exposure_colors
Character vector of colors used for exposure- difference curves. Named vectors are supported. The default reproduces the original manual palette.
- base_size
Positive finite base font size. Default is `10`.
- panel_labels
Character vector of length two used when both perspectives are combined. Default is `c("(a)", "(b)")`.
- label_size
Positive finite panel-label size. Default is `12`.
- rel_widths
Optional positive numeric vector controlling relative panel widths. By default, all displayed panels have equal width. Supply two values when two panels are displayed or three values when the overall ECI, lag contribution, and exposure-difference panels are displayed together.
Value
A ggplot/cowplot object. When both inputs are supplied, the returned object combines the overall ECI panel and the lag-specific panel. When only `eci_lag` is supplied, contribution and exposure-difference panels are combined. Component plots are stored in the `epiexposure_plot_components` attribute.