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Minor proposal for readability of CI lines in the zipper plot #55

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Dec 12, 2023
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Minor proposal for readability of CI lines in the zipper plot #55

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f6cc267
Minor proposal for readability of CI lines in the zipper plot
Dec 7, 2023
b8b6963
modifications as suggested by Alessandro
Dec 8, 2023
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5 changes: 3 additions & 2 deletions R/autoplot.simsum.R
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Expand Up @@ -10,6 +10,7 @@
#' @param top Should the legend for a nested loop plot be on the top side of the plot? Defaults to `TRUE`.
#' @param density.legend Should the legend for density and hexbin plots be included? Defaults to `TRUE`.
#' @param zoom A numeric value between 0 and 1 signalling that a zip plot should _zoom_ on the top x% of the plot (to ease interpretation). Defaults to 1, where the whole zip plot is displayed.
#' @param zip_ci_colors a string with a hex code if the CI intervals of the CI of the zipper plot are to be shown with one colour regardless of coverage, a list of 2 hex codes for optimal coverage (first) and over/under coverage (second) or a lsit of 3 hex codes for optimal coverage (first), uncercoverage(second) and overcoverage (third). Defaults to "yellow"
#' @param ... Not used.
#'
#' @return A `ggplot` object.
Expand All @@ -35,7 +36,7 @@
#' methodvar = "model", by = c("baseline", "ss", "esigma")
#' )
#' autoplot(s1, stats = "bias", type = "nlp")
autoplot.simsum <- function(object, type = "forest", stats = "nsim", target = NULL, fitted = TRUE, scales = "fixed", top = TRUE, density.legend = TRUE, zoom = 1, ...) {
autoplot.simsum <- function(object, type = "forest", stats = "nsim", target = NULL, fitted = TRUE, scales = "fixed", top = TRUE, density.legend = TRUE, zoom = 1, zip_ci_colors = "yellow", ...) {
# object <- s.nlp.subset
# type <- "nlp"
# stats <- "bias"
Expand Down Expand Up @@ -117,7 +118,7 @@ autoplot.simsum <- function(object, type = "forest", stats = "nsim", target = NU
plot <- switch(type,
"forest" = .forest_plot(data = df, methodvar = object$methodvar, by = object$by, stats = stats, ci = ci, target = target, scales = scales),
"lolly" = .lolly_plot(data = df, methodvar = object$methodvar, by = object$by, stats = stats, ci = ci, target = target, scales = scales),
"zip" = .zip_plot(data = object$x, estvarname = object$estvarname, se = object$se, true = object$true, methodvar = object$methodvar, by = object$by, ci.limits = object$ci.limits, df = object$df, control = object$control, summ = object$summ, zoom = zoom), # zip for coverage
"zip" = .zip_plot(data = object$x, estvarname = object$estvarname, se = object$se, true = object$true, methodvar = object$methodvar, by = object$by, ci.limits = object$ci.limits, df = object$df, control = object$control, summ = object$summ, zoom = zoom, zip_ci_colors = zip_ci_colors), # zip for coverage
"est" = .vs_plot(data = object$x, b = object$estvarname, methodvar = object$methodvar, by = object$by, fitted = fitted, scales = scales, ba = FALSE),
"se" = .vs_plot(data = object$x, b = object$se, methodvar = object$methodvar, by = object$by, fitted = fitted, scales = scales, ba = FALSE),
"est_ba" = .vs_plot(data = object$x, b = object$estvarname, methodvar = object$methodvar, by = object$by, fitted = fitted, scales = scales, ba = TRUE),
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35 changes: 28 additions & 7 deletions R/plot-types.R
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Expand Up @@ -76,7 +76,7 @@

### Zip plot
#' @keywords internal
.zip_plot <- function(data, estvarname, se, true, methodvar, by, ci.limits, df, control, summ, zoom) {
.zip_plot <- function(data, estvarname, se, true, methodvar, by, ci.limits, df, control, summ, zoom, zip_ci_colors) {
### Extract overall coverage
summ <- summ[summ$stat == "cover", ]
summ$cover <- summ$est
Expand Down Expand Up @@ -138,14 +138,35 @@
### Label of the y-axis
ylab <- ifelse(is.null(df), "Fractional centile of |z-score|", "Fractional centile of |t-score|")

### Define CI lines colors
if (length(zip_ci_colors) == 2) {
data$line_color_lower <- ifelse(data$cover_lower <= 0.95 & 0.95 <= data$cover_upper, zip_ci_colors[1], zip_ci_colors[2])
data$line_color_upper <- ifelse(data$cover_lower <= 0.95 & 0.95 <= data$cover_upper, zip_ci_colors[1], zip_ci_colors[2])

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} else if (length(zip_ci_colors) == 3) {
data$line_color_lower <- ifelse(data$cover_lower > 0.95 & data$cover_upper > 0.95, zip_ci_colors[3],
ifelse(data$cover_lower < 0.95 & data$cover_upper < 0.95, zip_ci_colors[2],
ifelse(data$cover_lower <= 0.95 & 0.95 <= data$cover_upper, zip_ci_colors[1], NA)))

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data$line_color_upper <- ifelse(data$cover_lower > 0.95 & data$cover_upper > 0.95, zip_ci_colors[3],
ifelse(data$cover_lower < 0.95 & data$cover_upper < 0.95, zip_ci_colors[2],
ifelse(data$cover_lower <= 0.95 & 0.95 <= data$cover_upper, zip_ci_colors[1], NA)))

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} else {
data$line_color_lower <- zip_ci_colors[1]
data$line_color_upper <- zip_ci_colors[1]
}




### Build plot
gg <- ggplot2::ggplot(data, ggplot2::aes(y = rank, x = lower, color = covering)) +
ggplot2::geom_segment(ggplot2::aes(yend = rank, xend = upper)) +
ggplot2::geom_vline(xintercept = true, color = "yellow", linetype = "dashed") +
ggplot2::geom_hline(ggplot2::aes(yintercept = cover_lower), color = "yellow", linetype = "dashed") +
ggplot2::geom_hline(ggplot2::aes(yintercept = cover_upper), color = "yellow", linetype = "dashed") +
ggplot2::labs(y = ylab, x = paste0(100 * control$level, "% confidence intervals"), color = "") +
theme(legend.position = "bottom")
ggplot2::geom_segment(ggplot2::aes(yend = rank, xend = upper)) +
ggplot2::geom_vline(xintercept = true, color = "black", linetype = "dashed") +
ggplot2::geom_hline(ggplot2::aes(yintercept = cover_lower), color = data$line_color_lower, linetype = "dashed", size = 1) +
ggplot2::geom_hline(ggplot2::aes(yintercept = 0.95), color = "black", linetype = "dashed") +
ggplot2::geom_hline(ggplot2::aes(yintercept = cover_upper), color = data$line_color_upper, linetype = "dashed", size = 1) +
ggplot2::labs(y = ylab, x = paste0(100 * control$level, "% confidence intervals"), color = "") +
theme(legend.position = "bottom")

### If 'by', use facet_grid; facet_wrap otherwise
if (!is.null(by) & !is.null(methodvar)) {
Expand Down
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