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#' Plot rankograms
#'
#' @description
#' This function produces a rankogram, i.e., an image plot of ranking
#' probabilities for all treatments.
#'
#' @param x An object of class \code{\link{rankogram}}.
#' @param type A character string specifying whether a "bar" chart, a
#' "line" graph, or "step" functions should be drawn. Can be
#' abbreviated.
#' @param pooled A character string indicating whether results for the
#' common (\code{"common"}) or random effects model (\code{"random"})
#' should be plotted. Can be abbreviated.
#' @param sort A logical indicating whether treatments should be
#' sorted by decreasing SUCRAs.
#' @param trts Treatment(s) to show in rankogram.
#' @param cumulative.rankprob A logical indicating whether cumulative
#' ranking probabilites should be shown.
#' @param ylim The y limits (min, max) of the plot.
#' @param ylab A label for the y-axis.
#' @param nchar.trts A numeric defining the minimum number of
#' characters used to create unique treatment names.
#' @param \dots Additional graphical arguments (ignored at the
#' moment).
#'
#' @details
#' This function produces an image plot of (cumulative) ranking
#' probabilities for all treatments as a bar graph, a line graph or as
#' step functions (argument \code{type}).
#'
#' By default (argument \code{pooled}), results for the random effects
#' model are shown if a network meta-analysis was conducted for both
#' the common and random effects model.
#'
#' Treatments are sorted according to their mean effects if argument
#' \code{sort = TRUE} (default). A subset of treatments can be
#' specified using argument \code{trts}.
#'
#' Cumulative ranking probabilites are shown if
#' \code{cumulative.rankprob = TRUE}. By default, step functions are
#' shown for cumulative ranking probabilites.
#'
#' @author Theodoros Papakonstantinou \email{dev@@tpapak.com}, Guido
#' Schwarzer \email{guido.schwarzer@@uniklinik-freiburg.de}
#'
#' @seealso \code{\link{rankogram}}
#'
#' @references
#' Salanti G, Ades AE, Ioannidis JP (2011):
#' Graphical methods and numerical summaries for presenting results
#' from multiple-treatment meta-analysis: an overview and tutorial.
#' \emph{Journal of Clinical Epidemiology},
#' \bold{64}, 163--71
#'
#' @examples
#' data(Woods2010)
#' p1 <- pairwise(treatment, event = r, n = N, studlab = author,
#' data = Woods2010, sm = "OR")
#' net1 <- netmeta(p1, small.values = "good")
#'
#' ran1 <- rankogram(net1, nsim = 100)
#' ran1
#'
#' plot(ran1)
#' plot(ran1, type = "l")
#' plot(ran1, cumulative.rankprob = TRUE)
#'
#' @method plot rankogram
#' @export
plot.rankogram <- function(x,
type = if (cumulative.rankprob) "step" else "bar",
pooled = ifelse(x$random, "random", "common"),
sort = TRUE, trts,
cumulative.rankprob = x$cumulative.rankprob,
ylim, ylab,
nchar.trts = x$nchar.trts, ...) {
chkclass(x, c("rankogram"))
x <- updateversion(x)
##
is.installed.package("gridExtra")
type <- setchar(type, c("bar", "line", "step"))
##
pooled <- setchar(pooled, c("common", "random", "fixed"))
pooled[pooled == "fixed"] <- "common"
##
chklogical(sort)
##
if (is.null(cumulative.rankprob))
cumulative.rankprob <- FALSE
chklogical(cumulative.rankprob)
##
missing.ylim <- missing(ylim)
if (!missing.ylim)
chknumeric(ylim, min = 0, max = 1, length = 2)
##
if (!missing(ylab))
chkchar(ylab, length = 1)
else {
if (cumulative.rankprob)
ylab <- "Cumulative\nprobability"
else
ylab <- "Probability"
}
if (missing(trts))
trts <- NULL
##
if (is.null(nchar.trts))
nchar.trts <- 666
chknumeric(nchar.trts, length = 1)
mytheme <-
theme(axis.line.x = ggplot2::element_line(colour = "black", size = 1,
linetype = "solid"),
axis.line.y = ggplot2::element_line(colour = "black", size = 1,
linetype = "solid"),
panel.grid.major = ggplot2::element_line(color = "transparent"),
panel.grid.minor = ggplot2::element_line(color = "transparent"),
panel.background = ggplot2::element_rect(fill = "transparent"),
plot.background = ggplot2::element_rect(
fill = "transparent",
colour = "transparent",
size = 1)
)
if (pooled == "random") {
if (cumulative.rankprob)
rankmatrix <- "cumrank.matrix.random"
else
rankmatrix <- "ranking.matrix.random"
##
sucras <- "ranking.random"
}
else if (pooled == "common") {
if (cumulative.rankprob)
rankmatrix <- "cumrank.matrix.common"
else
rankmatrix <- "ranking.matrix.common"
##
sucras <- "ranking.common"
}
##
if (is.null(x[[rankmatrix]]))
stop("No results for ", pooled, " effect",
if (pooled == "random") "s", " model available. ",
"Rerun rankogram() with argument '", pooled, " = TRUE'.",
call. = FALSE)
plotranks <- function(treat) {
df <- data.frame(pos = 1:nrow(x[[rankmatrix]]),
ranks = x[[rankmatrix]][treat, ])
mymaxvalue <- max(x[[rankmatrix]])
##
if (type == "bar")
p <- ggplot2::ggplot(mapping = aes(df$pos, df$ranks)) +
ggplot2::geom_col()
else if (type == "line")
p <- ggplot2::ggplot(mapping = aes(df$pos, df$ranks)) +
ggplot2::geom_line()
else if (type == "step")
p <- ggplot2::ggplot(mapping = aes(df$pos, df$ranks)) +
ggplot2::geom_step()
##
p <- p +
ggplot2::scale_x_continuous(breaks = seq(1, nrow(x[[rankmatrix]]), 1))
p <- p + ggplot2::labs(x = paste("Rank of", treats(treat, nchar.trts)))
p <- p + ggplot2::labs(y = ylab)
##
if (missing.ylim)
p <- p + ggplot2::expand_limits(x = c(1, x$x$n), y = c(0, mymaxvalue))
else
p <- p + ggplot2::expand_limits(x = c(1, x$x$n), y = ylim)
##
p + mytheme
}
##
if (sort)
treatnames <- names(sort(x[[sucras]], decreasing = TRUE))
else
treatnames <- names(x[[sucras]])
##
if (!is.null(trts)) {
trts.c <- setref(trts, treatnames, varname = "trts", length = 0)
treatnames <- treatnames[treatnames %in% trts.c]
}
##
rankplots <- do.call(gridExtra::grid.arrange, lapply(treatnames, plotranks))
}
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