R/forestplot2.R
In raredd/Gmisc0: Collection of functions for plotting relations, generating tables, and more.
#' Create a forest plot
#'
#' forestplot2 is based on the \pkg{rmeta} 2.16
#' \code{\link[rmeta]{forestplot}} function. This
#' function resolves some limitations of the original
#' functions such as:
#' \itemize{
#' \item{Adding expressions: }{Allows use of expressions, e.g. \code{expression(beta)}}
#' \item{Multiple bands: }{Using multiple confidence bands for the same label}
#' \item{Autosize: }{Adapts to windows size}
#' }
#'
#' Using multiple bands for the same label can be interesting when
#' one wants to compare different outcomer. It can also be an alternative
#' when you want to show both crude and adjusted estimates.
#'
#' Known issues: the x-axis does not entirely respect the margin.
#' Autosizing boxes is not always the best option, try to set these
#' manually as much as possible.
#'
#' @param labeltext A list, matrix, vector or expression with the names of each
#' row. The list should be wrapped in m x n number to resemble a matrix:
#' \code{list(list("rowname 1 col 1", "rowname 2 col 1"), list("r1c2", expression(beta))}
#' You can also provide a matrix although this cannot have expressions by design:
#' \code{matrix(c("rowname 1 col 1", "rowname 2 col 1", "r1c2", "beta"), ncol=2)}
#' Use NA:s for blank spaces and if you provide a full column with NA then
#' that column is a empty column that adds some space.
#' @param mean A vector or a matrix with the averages
#' @param lower The lower bound of the confidence interval for the forestplot, needs
#' to be the same format as the mean, i.e. matrix/vector of equal columns & length
#' @param upper The upper bound of the confidence interval for the forestplot, needs
#' to be the same format as the mean, i.e. matrix/vector of equal columns & length
#' @param align Vector giving alignment (l,r,c) for columns of table
#' @param is.summary A vector indicating by TRUE/FALSE if the value is a summary
#' value which means that it will have a different font-style.
#' @param fontfamily.summary The fontfamily of the summary
#' @param fontfamily.labelrow The fontfamily of a regular row
#' @param clip Lower and upper limits for clipping confidence intervals to arrows
#' @param xlab x-axis label
#' @param zero x-axis coordinate for zero line
#' @param graphwidth Width of confidence interval graph, see \code{\link{unit}} for
#' details on how to utilize mm etc. The default is \code{auto}, that is it uses up whatever
#' space that is left after adjusting for text size and legend.
#' @param lineheight Height of the graph. By default this is \code{auto} and adjustes to the
#' space that is left after adjusting for x-axis size and legend. Sometimes
#' it might be desireable to set the line height to a certain height, for
#' instance if you have several forestplots you may want to standardize their
#' line height, then you set this variable to a certain height, note this should
#' be provided as a \code{\link[grid]{unit}} object. A good option
#' is to set the line height to \code{unit(2, "cm")}. A third option
#' is to set line height to "lines" and then you get 50 % more than what the
#' text height is as your line height.
#' @param col See \code{\link{fpColors}}
#' @param xlog If TRUE, x-axis tick marks are exponentiated
#' @param xticks Optional user-specified x-axis tick marks. Specify NULL to use
#' the defaults, numeric(0) to omit the x-axis.
#' @param xticks.digits The number of digits to allow in the x-axis if this
#' is created by default.
#' @param lwd.xaxis lwd for the xaxis
#' @param lwd.zero lwd for the vertical line that gives the no-effect line
#' @param lwd.ci lwd for the confidence bands
#' @param cex The font adjustment
#' @param cex.axis The font adjustment for the x-xaxis, defaults to 60 \%
#' of the cex parameter.
#' @param boxsize Override the default box size based on precision
#' @param mar A numerical vector of the form c(bottom, left, top, right) of the type \code{unit()}
#' @param main The title of the plot if any, default \code{NULL}
#' @param legend Legen corresponding to the number of bars.
#' @param legend.pos The position of the legend, either at the "top" or the "right" unlesss
#' positioned inside the plot. If you want the legend to be positioned inside the plot
#' then you have to provide a list with the same x & y qualities as \code{\link[graphics]{legend}}.
#' For instance if you want the legend to be positioned at the top right corner then
#' use \code{legend.pos = list("topright")} - this is equivalent to \code{legend.pos = list(x=1, y=1)}.
#' If you want to have a distance from the edge of the graph then add a inset to the list,
#' e.g. \code{legend.pos = list("topright", "inset"=.1)} - the inset should be either a \code{\link[grid]{unit}}
#' element or a value between 0 and 1. The default is to have the boxes aligned vertical, if
#' you want them to be in a line then you can specify the "align" option, e.g.
#' \code{legend.pos = list("topright", "inset"=.1, "align"="horizontal")}
#' @param legend.cex The cex size of the legend, defaults to 80 \% procent of cex parameter.
#' @param legend.gp The \code{\link[grid]{gpar}} options for the legend. If you want
#' the background color to be light grey then use \code{legend.gp = gpar(fill = "lightgrey")}.
#' If you want a border then set the col argument: \code{legend.gp = gpar(fill = "lightgrey", col="black")}.
#' You can also use the lwd and lty argument as usual, \code{legend.gp = gpar(lwd=2, lty=1)}, will result
#' in a black border box of line type 1 and line width 2.
#' @param legend.r The box can have rounded edges, check out \code{\link[grid]{grid.roundrect}}. The
#' r option should be a \code{\link[grid]{unit}} object. This is by default \code{unit(0, "snpc")}
#' but you can choose any value that you want. The \code{"snpc"} unit is the preferred option.
#' @param legend.padding The padding for the legend box, only used if box is drawn. This is
#' the distance from the border to the text/boxes of the legend.
#' @param legend.title The title of the legend if any, default to NULL
#' @param new_page If you want the plot to appear on a new blank page then set this to \code{TRUE}, by
#' default it is \code{FALSE}.
#' @param confintNormalFn You can specify exactly how the line with the box is
#' drawn for the normal (i.e. non-summary) confidence interval by changing this
#' parameter to your own function or some of the alternatives provided in the package.
#' It defaults to the box function \code{\link{fpDrawNormalCI}}.
#' @param confintSummaryFn Same as previous argument but for the summary outputs
#' and it defaults to \code{\link{fpDrawSummaryCI}}.
#' @param legendMarkerFn What type of function should be used for drawing the
#' legends, this can be a list if you want different functions. It defaults to
#' a box if you have anything else than a single function or the number of columns
#' in the \code{mean} argument.
#' @param ... Passed on to the \code{confintNormalFn} and
#' \code{confintSummaryFn} arguments
#' @return void
#'
#' @import grid
#'
#' @author Max Gordon, Thomas Lumley
#'
#' @example inst/examples/forestplot2_example.R
#' @family forestplot functions
#' @export
forestplot2 <- function (labeltext,
mean, lower, upper,
align = NULL,
is.summary = FALSE,
fontfamily.summary = NULL,
fontfamily.labelrow = NULL,
clip = c(-Inf, Inf),
xlab = "",
zero = 0,
graphwidth = "auto",
lineheight = "auto",
col = fpColors(),
xlog = FALSE,
xticks = NULL,
xticks.digits = 2,
lwd.xaxis = NULL,
lwd.zero = NULL,
lwd.ci = NULL,
cex = 1,
cex.axis = cex * 0.6,
boxsize = NULL,
mar = unit(rep(5, times=4), "mm"),
main = NULL,
legend = NULL,
legend.pos = "top",
legend.cex = cex*.8,
legend.gp = NULL,
legend.r = unit(0, "snpc"),
legend.padding = unit(ifelse(length(legend.gp) > 0, 3, 0), "mm"),
legend.title = NULL,
new_page = FALSE,
confintNormalFn = fpDrawNormalCI,
confintSummaryFn = fpDrawSummaryCI,
legendMarkerFn = NULL,
...)
{
if (NCOL(mean) != NCOL(lower) ||
NCOL(lower) != NCOL(upper) ||
NCOL(mean) == 0)
stop('Mean, lower and upper contain invalid number of columns',
" Mean columns:", ncol(mean),
" Lower bound columns:", ncol(lower),
" Upper bound columns:", ncol(upper))
# Prepare the legend marker
if (!is.null(legend)){
legendMarkerFn <- prFpPrepareLegendMarker(legendMarkerFn = legendMarkerFn,
col_no = NCOL(mean),
confintNormalFn = confintNormalFn)
}
confintNormalFn <-
prFpGetConfintFnList(fn = confintNormalFn,
no_rows = NROW(mean),
no_cols = NCOL(mean))
confintSummaryFn <-
prFpGetConfintFnList(fn = confintSummaryFn,
no_rows = NROW(mean),
no_cols = NCOL(mean))
if (!is.unit(lineheight) && !lineheight %in% c("auto", "lines"))
stop("The argument lineheight must either be of type unit or set to 'auto',",
" you have provided a '", class(lineheight), "' class")
if (length(legend) > 0){
if (length(legend) != ncol(mean))
stop("If you want a legend you need to provide the same number of",
" legend descriptors as you have boxes per line, currently you have ",
ncol(mean), " boxes and ",
length(legend), " legends.")
if (is.list(legend.pos)){
legend.pos <- prFpGetLegendBoxPosition(legend.pos)
}else if (!legend.pos %in% c("top", "right")){
stop("The legend is either a list positioning it inside the main plot or at the 'top' or 'right' side,",
" the position '", legend.pos, "' is not valid.")
}
if (inherits(legend.gp, "gpar")){
# Remove default border if no color
# unless there is a line width or type specified
if (!"col" %in% names(legend.gp)){
if (any(c("lwd", "lwd") %in% names(legend.gp))){
legend.gp[["col"]] = "black"
}else{
legend.gp[["col"]] = NA
}
}
}
}
# Fix if data.frames were provided in the arguments
if (is.data.frame(mean))
mean <- as.matrix(mean)
if (is.data.frame(lower))
lower<- as.matrix(lower)
if (is.data.frame(upper))
upper <- as.matrix(upper)
# Save the original values since the function due to it's inheritance
# from the original forestplot needs some changing to the parameters
if (xlog){
# Change all the values along the log scale
org_mean <- log(mean)
org_lower <- log(lower)
org_upper <- log(upper)
}else{
org_mean <- mean
org_lower <- lower
org_upper <- upper
}
# For border calculations etc it's
# convenient to have the matrix as a
# vector
if (NCOL(mean) > 1){
mean <- as.vector(mean)
lower <- as.vector(lower)
upper <- as.vector(upper)
}
# Get the number of columns (nc) and number of rows (nr)
# if any columns are to be spacers the widthcolumn variable
if (is.expression(labeltext)){
widthcolumn <- c(TRUE)
# Can't figure out multiple levels of expressions
nc <- 1
nr <- length(labeltext)
label_type = "expression"
} else if (is.list(labeltext)){
if (!prFpValidateLabelList(labeltext))
stop("Invalid labellist, it has to be formed as a matrix m x n elements")
# Can't figure out multiple levels of expressions
nc <- length(labeltext)
widthcolumn = c()
# Should mark the columns that don't contain
# epressions, text or numbers as widthcolumns
for(col.no in seq(along=labeltext)){
empty_row <- TRUE
for (row.no in seq(along=labeltext[[col.no]])){
if (is.expression(labeltext[[col.no]][[row.no]]) ||
!is.na(labeltext[[col.no]][[row.no]])){
empty_row <- FALSE
break
}
}
widthcolumn <- append(widthcolumn, empty_row)
}
nr <- length(labeltext[[1]])
label_type = "list"
} else if (is.vector(labeltext)){
widthcolumn <- c(FALSE)
nc = 1
nr = length(labeltext)
labeltext <- matrix(labeltext, ncol=1)
label_type = "matrix"
} else {
# Original code for matrixes
widthcolumn <- !apply(is.na(labeltext), 1, any)
nc <- NCOL(labeltext)
nr <- NROW(labeltext)
label_type = "matrix"
}
# Prepare the summary and align variables
if (is.null(align)){
align <- c("l", rep("r", nc - 1))
} else {
align <- rep(align, length = nc)
}
is.summary <- rep(is.summary, length = nr)
labels <- prFpGetLabels(label_type = label_type,
labeltext = labeltext, align = align,
nc = nc, nr = nr,
is.summary = is.summary,
fontfamily.summary = fontfamily.summary,
fontfamily.labelrow = fontfamily.labelrow,
col = col, cex = cex)
# Set the gap between columns, I set it to
# 6 mm but for relative widths we switch it
# to npc that adapts to the window size
colgap <- convertUnit(unit(6, "mm"), "npc", valueOnly=TRUE)
if (colgap < .1)
colgap <- unit(.05, "npc")
else
colgap <- unit(colgap, "npc")
colgap <- convertUnit(colgap, "mm")
# There is always at least one column so grab the widest one
# and have that as the base for the column widths
colwidths <- unit.c(prFpFindWidestGrob(labels[[1]]), colgap)
# If multiple row label columns, add the other column widths
if (nc > 1) {
for (i in 2:nc){
colwidths <- unit.c(colwidths,
prFpFindWidestGrob(labels[[i]]),
colgap)
}
}
axisList <- prFpGetGraphTicksAndClips(xticks=xticks,
xticks.digits=xticks.digits,
xlog=xlog,
xlab=xlab,
lwd.xaxis=lwd.xaxis,
cex=cex,
cex.axis=cex.axis,
col=col,
clip=clip, zero=zero,
x_range=prFpXrange(upper = upper,
lower = lower,
clip = clip,
zero = zero,
xticks = xticks,
xlog = xlog),
nc = nc,
mean = org_mean)
clip <- axisList$clip
###################
# Create the plot #
###################
if (new_page) grid.newpage()
# Adjust for the margins and the x-axis + label
marList <- list()
# This breaks without separate variables
marList$bottom <- convertY(mar[1], "npc")
marList$left <- convertX(mar[2], "npc")
marList$top <- convertY(mar[3], "npc")
marList$right <- convertX(mar[4], "npc")
prPushMarginViewport(bottom = marList$bottom,
left = marList$left,
top = marList$top,
right = marList$right,
name="forestplot_margins")
if (is.character(main)){
prGridPlotTitle(title=main, base_cex = cex)
}
# Initiate the legend
if (length(legend) > 0){
lGrobs <- prFpGetLegendGrobs(legend = legend,
legend.cex = legend.cex,
legend.title = legend.title)
legend_horizontal_height <- sum(legend.padding,
attr(lGrobs, "max_height"),
legend.padding)
if (!is.null(attr(lGrobs, "title"))){
legend_horizontal_height <- sum(attr(lGrobs, "titleHeight"),
attr(lGrobs, "line_height_and_spacing")[2],
legend_horizontal_height)
}
legend_vertical_width <- sum(unit.c(legend.padding,
attr(lGrobs, "max_height"),
colgap,
attr(lGrobs, "max_width"),
legend.padding))
# Prepare the viewports if the legend is not
# positioned inside the forestplot, i.e. on the top or right side
if ((!is.list(legend.pos) && legend.pos == "top") ||
("align" %in% names(legend.pos) && legend.pos[["align"]] == "horizontal")){
legend_layout <- grid.layout(nrow=3, ncol=1,
heights=unit.c(legend_horizontal_height,
colgap+colgap,
unit(1, "npc")-
legend_horizontal_height-
colgap-colgap))
legend_pos <- list(row = 1,
col = 1)
main_pos <- list(row = 3,
col = 1)
}else{
legend_layout <- grid.layout(nrow=1, ncol=3,
widths = unit.c(unit(1, "npc") -
colgap -
legend_vertical_width,
colgap,
legend_vertical_width))
legend_pos <- list(row = 1,
col = 3)
main_pos <- list(row = 1,
col = 1)
}
}
# If the legend should be positioned within the plot then wait
# until after the plot has been drawn
if (length(legend) > 0 && !is.list(legend.pos)){
pushViewport(prFpGetLayoutVP(lineheight=lineheight,
labels = labels,
nr=nr,
legend_layout=legend_layout))
vp <- viewport(layout.pos.row = legend_pos$row,
layout.pos.col = legend_pos$col,
name = "legend")
pushViewport(vp)
# Draw the legend
prFpDrawLegend(lGrobs = lGrobs,
legend.pos = legend.pos,
col = col,
colgap = convertUnit(colgap, unitTo="mm"),
legend.gp = legend.gp,
legend.r = legend.r,
legend.padding = legend.padding,
legendMarkerFn = legendMarkerFn,
...)
upViewport()
# Reset to the main plot
vp <- viewport(layout.pos.row = main_pos$row,
layout.pos.col = main_pos$col,
name="main")
pushViewport(vp)
}else{
pushViewport(prFpGetLayoutVP(lineheight=lineheight,
labels = labels, nr=nr))
}
###########################################
# Normalize the widths to cover the whole #
# width of the graph space. #
###########################################
if (is.unit(graphwidth)){
# Add the base grapwh width to the total column width
# default is 2 inches
colwidths <- unit.c(colwidths, graphwidth)
npc_colwidths <- convertUnit(colwidths, "npc", valueOnly=TRUE)
colwidths <- unit(npc_colwidths/sum(npc_colwidths), "npc")
}else if(graphwidth=="auto"){
# If graph width is not provided as a unit the autosize it to the
# rest of the space available
npc_colwidths <- convertUnit(colwidths, "npc", valueOnly=TRUE)
graphwidth <- unit(1 - sum(npc_colwidths), "npc")
colwidths <- unit.c(colwidths, graphwidth)
}else{
stop("You have to provide graph width either as a unit() object or as auto.",
" Auto sizes the graph to maximally use the available space.",
" If you want to have exact mm width then use graphwidth = unit(34, 'mm').")
}
# Add space for the axis and the label
axis_height <- unit(0, "npc")
if (is.grob(axisList$axisGrob))
axis_height <- axis_height + grobHeight(axisList$axisGrob)
if (is.grob(axisList$labGrob)){
gp_lab_cex <- prGetTextGrobCex(axisList$labGrob)
# The lab grob y actually includes the axis (note negative)
axis_height <- axis_height +
unit(gp_lab_cex+.5, "line")
}
axis_layout <- grid.layout(nrow=2,
ncol=1,
heights=unit.c(unit(1, "npc") - axis_height,
axis_height))
pushViewport(viewport(layout=axis_layout,
name="axis_margin"))
pushViewport(viewport(layout.pos.row=1, layout.pos.col=1))
# The base viewport, set the increase.line_height paremeter if it seems a little
# crowded between the lines that might happen when having multiple comparisons
main_grid_layout <- grid.layout(nrow = nr,
ncol = length(colwidths),
widths = colwidths,
heights = unit(rep(1/nr, nr), "npc"),
respect = TRUE)
pushViewport(viewport(layout = main_grid_layout,
name="BaseGrid"))
# Create the fourth argument 4 the fpDrawNormalCI() function
if (!is.null(boxsize)){
# If matrix is provided this will convert it
# to a vector but it doesn't matter in this case
info <- rep(boxsize, length = length(mean))
}else{
# Get width of the lines
cwidth <- (upper - lower)
# Set cwidth to min value if the value is invalid
# this can be the case for reference points
cwidth[cwidth <= 0 | is.na(cwidth)] <- min(cwidth[cwidth > 0])
textHeight <- convertUnit(grobHeight(textGrob("A", gp=gpar(cex=cex))),
unitTo="npc",
valueOnly=TRUE)
info <- 1/cwidth*0.75
info <- info/max(info[!is.summary], na.rm = TRUE)
# Adjust the dots as it gets ridiculous with small text and huge dots
if (any(textHeight*(nr+.5) * 1.5 < info))
info <- textHeight*(nr+.5) * 1.5 * info/max(info, na.rm=TRUE) + textHeight*(nr+.5)*1.5/4
# Set summary to maximum size
info[is.summary] <- 1/NCOL(org_mean)
}
prFpPrintLabels(labels=labels,
nc=nc,
nr=nr)
prFpPrintXaxis(axisList=axisList,
col=col, lwd.zero=lwd.zero)
# Output the different confidence intervals
for (i in 1:nr) {
if (is.na(mean[i]))
next
if (is.matrix(org_mean)){
low_values <- org_lower[i,]
mean_values <- org_mean[i,]
up_values <- org_upper[i,]
info_values <- matrix(info, ncol=length(low_values))[i, ]
}else{
low_values <- org_lower[i]
mean_values <- org_mean[i]
up_values <- org_upper[i]
info_values <- info[i]
}
# The line and box colors may vary
clr.line <- rep(col$line, length.out=length(low_values))
clr.marker <- rep(col$box, length.out=length(low_values))
clr.summary <- rep(col$summary, length.out=length(low_values))
line_vp <- viewport(layout.pos.row = i,
layout.pos.col = length(colwidths),
xscale = axisList$x_range,
name = sprintf("Line_%d_%d", i, 2 * nc + 1))
pushViewport(line_vp)
# Draw multiple confidence intervals
if (length(low_values) > 1){
b_height <- max(info_values)
if (is.unit(b_height))
b_height <- convertUnit(b_height, unitTo="npc", valueOnly=TRUE)
# Add some space so that the boxes
# between lines don't blend
margin <- 0.05
y.offset_base <- b_height/2 + margin
y.offset_increase <- (1 - margin - y.offset_base*2)/(length(low_values)-1)
for(j in length(low_values):1){
# Start from the bottom and plot up
# the one on top should always be
# above the one below
current_y.offset <- y.offset_base + (length(low_values)-j)*y.offset_increase
if (is.summary[i]){
call_list <-
list(confintSummaryFn[[i]][[j]],
lower_limit=low_values[j],
estimate=mean_values[j],
upper_limit=up_values[j],
size=info_values[j],
col = clr.summary[j],
y.offset = current_y.offset)
}else{
call_list <-
list(confintNormalFn[[i]][[j]],
lower_limit=low_values[j],
estimate=mean_values[j],
upper_limit=up_values[j],
size=info_values[j],
y.offset = current_y.offset,
clr.line = clr.line[j],
clr.marker = clr.marker[j],
lwd=lwd.ci)
}
# Add additional arguments that are passed on
# from the original parameters
if (length(list(...)) > 0){
ll <- list(...)
for (name in names(ll)){
call_list[[name]] <- ll[[name]]
}
}
# Do the actual drawing of the object
eval(as.call(call_list))
}
}else{
if (is.summary[i]){
call_list <-
list(confintSummaryFn[[i]],
lower_limit=low_values,
estimate=mean_values,
upper_limit=up_values,
size=info_values,
col=clr.summary)
}else{
call_list <-
list(confintNormalFn[[i]],
lower_limit=low_values,
estimate=mean_values,
upper_limit=up_values,
size=info_values,
clr.line = clr.line,
clr.marker = clr.marker,
lwd=lwd.ci)
}
# Add additional arguments that are passed on
# from the original parameters
if (length(list(...)) > 0){
ll <- list(...)
for (name in names(ll)){
call_list[[name]] <- ll[[name]]
}
}
# Do the actual drawing of the object
eval(as.call(call_list))
}
upViewport()
}
# Output the legend if it is inside the main plot
if (length(legend) > 0 && is.list(legend.pos)){
plot_vp <- viewport(layout.pos.row = 1:nr,
layout.pos.col = 2 * nc + 1,
name = "main_plot_area")
pushViewport(plot_vp)
if ("align" %in% names(legend.pos) && legend.pos[["align"]] == "horizontal"){
# Calculated with padding above
height <- legend_horizontal_height
# Calculate the horizontal width by iterating througha all elements
# as each element may have a different width
width <- 0
for (i in 1:length(lGrobs)){
if (width > 0){
width <- width + convertUnit(colgap, unitTo="npc", valueOnly=TRUE)
}
width <- width + convertUnit(attr(lGrobs, "max_height") + colgap + attr(lGrobs[[i]], "width"), unitTo="npc", valueOnly=TRUE)
}
# Add the padding
width <- unit(width + convertUnit(legend.padding, unitTo="npc", valueOnly=TRUE)*2, "npc")
}else{
legend_height <- attr(lGrobs, "line_height_and_spacing")[rep(1:2, length.out=length(legend)*2-1)]
if (!is.null(attr(lGrobs, "title"))){
legend_height <- unit.c(attr(lGrobs, "titleHeight"),
attr(lGrobs, "line_height_and_spacing")[2], legend_height)
}
height <- sum(legend.padding, legend_height, legend.padding)
width <- legend_vertical_width
}
pushViewport(viewport(x=legend.pos[["x"]],
y=legend.pos[["y"]],
width=width,
height=height,
just=legend.pos[["just"]]))
# Draw the legend
prFpDrawLegend(lGrobs = lGrobs,
legend.pos = legend.pos,
col = col,
colgap = colgap,
legend.gp = legend.gp,
legend.r = legend.r,
legend.padding = legend.padding,
legendMarkerFn = legendMarkerFn,
...)
upViewport(2)
}
# Go back to the original viewport
seekViewport("forestplot_margins")
upViewport(2)
}
raredd/Gmisc0 documentation built on May 27, 2019, 2:02 a.m.
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#' Create a forest plot
#'
#' forestplot2 is based on the \pkg{rmeta} 2.16
#' \code{\link[rmeta]{forestplot}} function. This
#' function resolves some limitations of the original
#' functions such as:
#' \itemize{
#' \item{Adding expressions: }{Allows use of expressions, e.g. \code{expression(beta)}}
#' \item{Multiple bands: }{Using multiple confidence bands for the same label}
#' \item{Autosize: }{Adapts to windows size}
#' }
#'
#' Using multiple bands for the same label can be interesting when
#' one wants to compare different outcomer. It can also be an alternative
#' when you want to show both crude and adjusted estimates.
#'
#' Known issues: the x-axis does not entirely respect the margin.
#' Autosizing boxes is not always the best option, try to set these
#' manually as much as possible.
#'
#' @param labeltext A list, matrix, vector or expression with the names of each
#' row. The list should be wrapped in m x n number to resemble a matrix:
#' \code{list(list("rowname 1 col 1", "rowname 2 col 1"), list("r1c2", expression(beta))}
#' You can also provide a matrix although this cannot have expressions by design:
#' \code{matrix(c("rowname 1 col 1", "rowname 2 col 1", "r1c2", "beta"), ncol=2)}
#' Use NA:s for blank spaces and if you provide a full column with NA then
#' that column is a empty column that adds some space.
#' @param mean A vector or a matrix with the averages
#' @param lower The lower bound of the confidence interval for the forestplot, needs
#' to be the same format as the mean, i.e. matrix/vector of equal columns & length
#' @param upper The upper bound of the confidence interval for the forestplot, needs
#' to be the same format as the mean, i.e. matrix/vector of equal columns & length
#' @param align Vector giving alignment (l,r,c) for columns of table
#' @param is.summary A vector indicating by TRUE/FALSE if the value is a summary
#' value which means that it will have a different font-style.
#' @param fontfamily.summary The fontfamily of the summary
#' @param fontfamily.labelrow The fontfamily of a regular row
#' @param clip Lower and upper limits for clipping confidence intervals to arrows
#' @param xlab x-axis label
#' @param zero x-axis coordinate for zero line
#' @param graphwidth Width of confidence interval graph, see \code{\link{unit}} for
#' details on how to utilize mm etc. The default is \code{auto}, that is it uses up whatever
#' space that is left after adjusting for text size and legend.
#' @param lineheight Height of the graph. By default this is \code{auto} and adjustes to the
#' space that is left after adjusting for x-axis size and legend. Sometimes
#' it might be desireable to set the line height to a certain height, for
#' instance if you have several forestplots you may want to standardize their
#' line height, then you set this variable to a certain height, note this should
#' be provided as a \code{\link[grid]{unit}} object. A good option
#' is to set the line height to \code{unit(2, "cm")}. A third option
#' is to set line height to "lines" and then you get 50 % more than what the
#' text height is as your line height.
#' @param col See \code{\link{fpColors}}
#' @param xlog If TRUE, x-axis tick marks are exponentiated
#' @param xticks Optional user-specified x-axis tick marks. Specify NULL to use
#' the defaults, numeric(0) to omit the x-axis.
#' @param xticks.digits The number of digits to allow in the x-axis if this
#' is created by default.
#' @param lwd.xaxis lwd for the xaxis
#' @param lwd.zero lwd for the vertical line that gives the no-effect line
#' @param lwd.ci lwd for the confidence bands
#' @param cex The font adjustment
#' @param cex.axis The font adjustment for the x-xaxis, defaults to 60 \%
#' of the cex parameter.
#' @param boxsize Override the default box size based on precision
#' @param mar A numerical vector of the form c(bottom, left, top, right) of the type \code{unit()}
#' @param main The title of the plot if any, default \code{NULL}
#' @param legend Legen corresponding to the number of bars.
#' @param legend.pos The position of the legend, either at the "top" or the "right" unlesss
#' positioned inside the plot. If you want the legend to be positioned inside the plot
#' then you have to provide a list with the same x & y qualities as \code{\link[graphics]{legend}}.
#' For instance if you want the legend to be positioned at the top right corner then
#' use \code{legend.pos = list("topright")} - this is equivalent to \code{legend.pos = list(x=1, y=1)}.
#' If you want to have a distance from the edge of the graph then add a inset to the list,
#' e.g. \code{legend.pos = list("topright", "inset"=.1)} - the inset should be either a \code{\link[grid]{unit}}
#' element or a value between 0 and 1. The default is to have the boxes aligned vertical, if
#' you want them to be in a line then you can specify the "align" option, e.g.
#' \code{legend.pos = list("topright", "inset"=.1, "align"="horizontal")}
#' @param legend.cex The cex size of the legend, defaults to 80 \% procent of cex parameter.
#' @param legend.gp The \code{\link[grid]{gpar}} options for the legend. If you want
#' the background color to be light grey then use \code{legend.gp = gpar(fill = "lightgrey")}.
#' If you want a border then set the col argument: \code{legend.gp = gpar(fill = "lightgrey", col="black")}.
#' You can also use the lwd and lty argument as usual, \code{legend.gp = gpar(lwd=2, lty=1)}, will result
#' in a black border box of line type 1 and line width 2.
#' @param legend.r The box can have rounded edges, check out \code{\link[grid]{grid.roundrect}}. The
#' r option should be a \code{\link[grid]{unit}} object. This is by default \code{unit(0, "snpc")}
#' but you can choose any value that you want. The \code{"snpc"} unit is the preferred option.
#' @param legend.padding The padding for the legend box, only used if box is drawn. This is
#' the distance from the border to the text/boxes of the legend.
#' @param legend.title The title of the legend if any, default to NULL
#' @param new_page If you want the plot to appear on a new blank page then set this to \code{TRUE}, by
#' default it is \code{FALSE}.
#' @param confintNormalFn You can specify exactly how the line with the box is
#' drawn for the normal (i.e. non-summary) confidence interval by changing this
#' parameter to your own function or some of the alternatives provided in the package.
#' It defaults to the box function \code{\link{fpDrawNormalCI}}.
#' @param confintSummaryFn Same as previous argument but for the summary outputs
#' and it defaults to \code{\link{fpDrawSummaryCI}}.
#' @param legendMarkerFn What type of function should be used for drawing the
#' legends, this can be a list if you want different functions. It defaults to
#' a box if you have anything else than a single function or the number of columns
#' in the \code{mean} argument.
#' @param ... Passed on to the \code{confintNormalFn} and
#' \code{confintSummaryFn} arguments
#' @return void
#'
#' @import grid
#'
#' @author Max Gordon, Thomas Lumley
#'
#' @example inst/examples/forestplot2_example.R
#' @family forestplot functions
#' @export
forestplot2 <- function (labeltext,
mean, lower, upper,
align = NULL,
is.summary = FALSE,
fontfamily.summary = NULL,
fontfamily.labelrow = NULL,
clip = c(-Inf, Inf),
xlab = "",
zero = 0,
graphwidth = "auto",
lineheight = "auto",
col = fpColors(),
xlog = FALSE,
xticks = NULL,
xticks.digits = 2,
lwd.xaxis = NULL,
lwd.zero = NULL,
lwd.ci = NULL,
cex = 1,
cex.axis = cex * 0.6,
boxsize = NULL,
mar = unit(rep(5, times=4), "mm"),
main = NULL,
legend = NULL,
legend.pos = "top",
legend.cex = cex*.8,
legend.gp = NULL,
legend.r = unit(0, "snpc"),
legend.padding = unit(ifelse(length(legend.gp) > 0, 3, 0), "mm"),
legend.title = NULL,
new_page = FALSE,
confintNormalFn = fpDrawNormalCI,
confintSummaryFn = fpDrawSummaryCI,
legendMarkerFn = NULL,
...)
{
if (NCOL(mean) != NCOL(lower) ||
NCOL(lower) != NCOL(upper) ||
NCOL(mean) == 0)
stop('Mean, lower and upper contain invalid number of columns',
" Mean columns:", ncol(mean),
" Lower bound columns:", ncol(lower),
" Upper bound columns:", ncol(upper))
# Prepare the legend marker
if (!is.null(legend)){
legendMarkerFn <- prFpPrepareLegendMarker(legendMarkerFn = legendMarkerFn,
col_no = NCOL(mean),
confintNormalFn = confintNormalFn)
}
confintNormalFn <-
prFpGetConfintFnList(fn = confintNormalFn,
no_rows = NROW(mean),
no_cols = NCOL(mean))
confintSummaryFn <-
prFpGetConfintFnList(fn = confintSummaryFn,
no_rows = NROW(mean),
no_cols = NCOL(mean))
if (!is.unit(lineheight) && !lineheight %in% c("auto", "lines"))
stop("The argument lineheight must either be of type unit or set to 'auto',",
" you have provided a '", class(lineheight), "' class")
if (length(legend) > 0){
if (length(legend) != ncol(mean))
stop("If you want a legend you need to provide the same number of",
" legend descriptors as you have boxes per line, currently you have ",
ncol(mean), " boxes and ",
length(legend), " legends.")
if (is.list(legend.pos)){
legend.pos <- prFpGetLegendBoxPosition(legend.pos)
}else if (!legend.pos %in% c("top", "right")){
stop("The legend is either a list positioning it inside the main plot or at the 'top' or 'right' side,",
" the position '", legend.pos, "' is not valid.")
}
if (inherits(legend.gp, "gpar")){
# Remove default border if no color
# unless there is a line width or type specified
if (!"col" %in% names(legend.gp)){
if (any(c("lwd", "lwd") %in% names(legend.gp))){
legend.gp[["col"]] = "black"
}else{
legend.gp[["col"]] = NA
}
}
}
}
# Fix if data.frames were provided in the arguments
if (is.data.frame(mean))
mean <- as.matrix(mean)
if (is.data.frame(lower))
lower<- as.matrix(lower)
if (is.data.frame(upper))
upper <- as.matrix(upper)
# Save the original values since the function due to it's inheritance
# from the original forestplot needs some changing to the parameters
if (xlog){
# Change all the values along the log scale
org_mean <- log(mean)
org_lower <- log(lower)
org_upper <- log(upper)
}else{
org_mean <- mean
org_lower <- lower
org_upper <- upper
}
# For border calculations etc it's
# convenient to have the matrix as a
# vector
if (NCOL(mean) > 1){
mean <- as.vector(mean)
lower <- as.vector(lower)
upper <- as.vector(upper)
}
# Get the number of columns (nc) and number of rows (nr)
# if any columns are to be spacers the widthcolumn variable
if (is.expression(labeltext)){
widthcolumn <- c(TRUE)
# Can't figure out multiple levels of expressions
nc <- 1
nr <- length(labeltext)
label_type = "expression"
} else if (is.list(labeltext)){
if (!prFpValidateLabelList(labeltext))
stop("Invalid labellist, it has to be formed as a matrix m x n elements")
# Can't figure out multiple levels of expressions
nc <- length(labeltext)
widthcolumn = c()
# Should mark the columns that don't contain
# epressions, text or numbers as widthcolumns
for(col.no in seq(along=labeltext)){
empty_row <- TRUE
for (row.no in seq(along=labeltext[[col.no]])){
if (is.expression(labeltext[[col.no]][[row.no]]) ||
!is.na(labeltext[[col.no]][[row.no]])){
empty_row <- FALSE
break
}
}
widthcolumn <- append(widthcolumn, empty_row)
}
nr <- length(labeltext[[1]])
label_type = "list"
} else if (is.vector(labeltext)){
widthcolumn <- c(FALSE)
nc = 1
nr = length(labeltext)
labeltext <- matrix(labeltext, ncol=1)
label_type = "matrix"
} else {
# Original code for matrixes
widthcolumn <- !apply(is.na(labeltext), 1, any)
nc <- NCOL(labeltext)
nr <- NROW(labeltext)
label_type = "matrix"
}
# Prepare the summary and align variables
if (is.null(align)){
align <- c("l", rep("r", nc - 1))
} else {
align <- rep(align, length = nc)
}
is.summary <- rep(is.summary, length = nr)
labels <- prFpGetLabels(label_type = label_type,
labeltext = labeltext, align = align,
nc = nc, nr = nr,
is.summary = is.summary,
fontfamily.summary = fontfamily.summary,
fontfamily.labelrow = fontfamily.labelrow,
col = col, cex = cex)
# Set the gap between columns, I set it to
# 6 mm but for relative widths we switch it
# to npc that adapts to the window size
colgap <- convertUnit(unit(6, "mm"), "npc", valueOnly=TRUE)
if (colgap < .1)
colgap <- unit(.05, "npc")
else
colgap <- unit(colgap, "npc")
colgap <- convertUnit(colgap, "mm")
# There is always at least one column so grab the widest one
# and have that as the base for the column widths
colwidths <- unit.c(prFpFindWidestGrob(labels[[1]]), colgap)
# If multiple row label columns, add the other column widths
if (nc > 1) {
for (i in 2:nc){
colwidths <- unit.c(colwidths,
prFpFindWidestGrob(labels[[i]]),
colgap)
}
}
axisList <- prFpGetGraphTicksAndClips(xticks=xticks,
xticks.digits=xticks.digits,
xlog=xlog,
xlab=xlab,
lwd.xaxis=lwd.xaxis,
cex=cex,
cex.axis=cex.axis,
col=col,
clip=clip, zero=zero,
x_range=prFpXrange(upper = upper,
lower = lower,
clip = clip,
zero = zero,
xticks = xticks,
xlog = xlog),
nc = nc,
mean = org_mean)
clip <- axisList$clip
###################
# Create the plot #
###################
if (new_page) grid.newpage()
# Adjust for the margins and the x-axis + label
marList <- list()
# This breaks without separate variables
marList$bottom <- convertY(mar[1], "npc")
marList$left <- convertX(mar[2], "npc")
marList$top <- convertY(mar[3], "npc")
marList$right <- convertX(mar[4], "npc")
prPushMarginViewport(bottom = marList$bottom,
left = marList$left,
top = marList$top,
right = marList$right,
name="forestplot_margins")
if (is.character(main)){
prGridPlotTitle(title=main, base_cex = cex)
}
# Initiate the legend
if (length(legend) > 0){
lGrobs <- prFpGetLegendGrobs(legend = legend,
legend.cex = legend.cex,
legend.title = legend.title)
legend_horizontal_height <- sum(legend.padding,
attr(lGrobs, "max_height"),
legend.padding)
if (!is.null(attr(lGrobs, "title"))){
legend_horizontal_height <- sum(attr(lGrobs, "titleHeight"),
attr(lGrobs, "line_height_and_spacing")[2],
legend_horizontal_height)
}
legend_vertical_width <- sum(unit.c(legend.padding,
attr(lGrobs, "max_height"),
colgap,
attr(lGrobs, "max_width"),
legend.padding))
# Prepare the viewports if the legend is not
# positioned inside the forestplot, i.e. on the top or right side
if ((!is.list(legend.pos) && legend.pos == "top") ||
("align" %in% names(legend.pos) && legend.pos[["align"]] == "horizontal")){
legend_layout <- grid.layout(nrow=3, ncol=1,
heights=unit.c(legend_horizontal_height,
colgap+colgap,
unit(1, "npc")-
legend_horizontal_height-
colgap-colgap))
legend_pos <- list(row = 1,
col = 1)
main_pos <- list(row = 3,
col = 1)
}else{
legend_layout <- grid.layout(nrow=1, ncol=3,
widths = unit.c(unit(1, "npc") -
colgap -
legend_vertical_width,
colgap,
legend_vertical_width))
legend_pos <- list(row = 1,
col = 3)
main_pos <- list(row = 1,
col = 1)
}
}
# If the legend should be positioned within the plot then wait
# until after the plot has been drawn
if (length(legend) > 0 && !is.list(legend.pos)){
pushViewport(prFpGetLayoutVP(lineheight=lineheight,
labels = labels,
nr=nr,
legend_layout=legend_layout))
vp <- viewport(layout.pos.row = legend_pos$row,
layout.pos.col = legend_pos$col,
name = "legend")
pushViewport(vp)
# Draw the legend
prFpDrawLegend(lGrobs = lGrobs,
legend.pos = legend.pos,
col = col,
colgap = convertUnit(colgap, unitTo="mm"),
legend.gp = legend.gp,
legend.r = legend.r,
legend.padding = legend.padding,
legendMarkerFn = legendMarkerFn,
...)
upViewport()
# Reset to the main plot
vp <- viewport(layout.pos.row = main_pos$row,
layout.pos.col = main_pos$col,
name="main")
pushViewport(vp)
}else{
pushViewport(prFpGetLayoutVP(lineheight=lineheight,
labels = labels, nr=nr))
}
###########################################
# Normalize the widths to cover the whole #
# width of the graph space. #
###########################################
if (is.unit(graphwidth)){
# Add the base grapwh width to the total column width
# default is 2 inches
colwidths <- unit.c(colwidths, graphwidth)
npc_colwidths <- convertUnit(colwidths, "npc", valueOnly=TRUE)
colwidths <- unit(npc_colwidths/sum(npc_colwidths), "npc")
}else if(graphwidth=="auto"){
# If graph width is not provided as a unit the autosize it to the
# rest of the space available
npc_colwidths <- convertUnit(colwidths, "npc", valueOnly=TRUE)
graphwidth <- unit(1 - sum(npc_colwidths), "npc")
colwidths <- unit.c(colwidths, graphwidth)
}else{
stop("You have to provide graph width either as a unit() object or as auto.",
" Auto sizes the graph to maximally use the available space.",
" If you want to have exact mm width then use graphwidth = unit(34, 'mm').")
}
# Add space for the axis and the label
axis_height <- unit(0, "npc")
if (is.grob(axisList$axisGrob))
axis_height <- axis_height + grobHeight(axisList$axisGrob)
if (is.grob(axisList$labGrob)){
gp_lab_cex <- prGetTextGrobCex(axisList$labGrob)
# The lab grob y actually includes the axis (note negative)
axis_height <- axis_height +
unit(gp_lab_cex+.5, "line")
}
axis_layout <- grid.layout(nrow=2,
ncol=1,
heights=unit.c(unit(1, "npc") - axis_height,
axis_height))
pushViewport(viewport(layout=axis_layout,
name="axis_margin"))
pushViewport(viewport(layout.pos.row=1, layout.pos.col=1))
# The base viewport, set the increase.line_height paremeter if it seems a little
# crowded between the lines that might happen when having multiple comparisons
main_grid_layout <- grid.layout(nrow = nr,
ncol = length(colwidths),
widths = colwidths,
heights = unit(rep(1/nr, nr), "npc"),
respect = TRUE)
pushViewport(viewport(layout = main_grid_layout,
name="BaseGrid"))
# Create the fourth argument 4 the fpDrawNormalCI() function
if (!is.null(boxsize)){
# If matrix is provided this will convert it
# to a vector but it doesn't matter in this case
info <- rep(boxsize, length = length(mean))
}else{
# Get width of the lines
cwidth <- (upper - lower)
# Set cwidth to min value if the value is invalid
# this can be the case for reference points
cwidth[cwidth <= 0 | is.na(cwidth)] <- min(cwidth[cwidth > 0])
textHeight <- convertUnit(grobHeight(textGrob("A", gp=gpar(cex=cex))),
unitTo="npc",
valueOnly=TRUE)
info <- 1/cwidth*0.75
info <- info/max(info[!is.summary], na.rm = TRUE)
# Adjust the dots as it gets ridiculous with small text and huge dots
if (any(textHeight*(nr+.5) * 1.5 < info))
info <- textHeight*(nr+.5) * 1.5 * info/max(info, na.rm=TRUE) + textHeight*(nr+.5)*1.5/4
# Set summary to maximum size
info[is.summary] <- 1/NCOL(org_mean)
}
prFpPrintLabels(labels=labels,
nc=nc,
nr=nr)
prFpPrintXaxis(axisList=axisList,
col=col, lwd.zero=lwd.zero)
# Output the different confidence intervals
for (i in 1:nr) {
if (is.na(mean[i]))
next
if (is.matrix(org_mean)){
low_values <- org_lower[i,]
mean_values <- org_mean[i,]
up_values <- org_upper[i,]
info_values <- matrix(info, ncol=length(low_values))[i, ]
}else{
low_values <- org_lower[i]
mean_values <- org_mean[i]
up_values <- org_upper[i]
info_values <- info[i]
}
# The line and box colors may vary
clr.line <- rep(col$line, length.out=length(low_values))
clr.marker <- rep(col$box, length.out=length(low_values))
clr.summary <- rep(col$summary, length.out=length(low_values))
line_vp <- viewport(layout.pos.row = i,
layout.pos.col = length(colwidths),
xscale = axisList$x_range,
name = sprintf("Line_%d_%d", i, 2 * nc + 1))
pushViewport(line_vp)
# Draw multiple confidence intervals
if (length(low_values) > 1){
b_height <- max(info_values)
if (is.unit(b_height))
b_height <- convertUnit(b_height, unitTo="npc", valueOnly=TRUE)
# Add some space so that the boxes
# between lines don't blend
margin <- 0.05
y.offset_base <- b_height/2 + margin
y.offset_increase <- (1 - margin - y.offset_base*2)/(length(low_values)-1)
for(j in length(low_values):1){
# Start from the bottom and plot up
# the one on top should always be
# above the one below
current_y.offset <- y.offset_base + (length(low_values)-j)*y.offset_increase
if (is.summary[i]){
call_list <-
list(confintSummaryFn[[i]][[j]],
lower_limit=low_values[j],
estimate=mean_values[j],
upper_limit=up_values[j],
size=info_values[j],
col = clr.summary[j],
y.offset = current_y.offset)
}else{
call_list <-
list(confintNormalFn[[i]][[j]],
lower_limit=low_values[j],
estimate=mean_values[j],
upper_limit=up_values[j],
size=info_values[j],
y.offset = current_y.offset,
clr.line = clr.line[j],
clr.marker = clr.marker[j],
lwd=lwd.ci)
}
# Add additional arguments that are passed on
# from the original parameters
if (length(list(...)) > 0){
ll <- list(...)
for (name in names(ll)){
call_list[[name]] <- ll[[name]]
}
}
# Do the actual drawing of the object
eval(as.call(call_list))
}
}else{
if (is.summary[i]){
call_list <-
list(confintSummaryFn[[i]],
lower_limit=low_values,
estimate=mean_values,
upper_limit=up_values,
size=info_values,
col=clr.summary)
}else{
call_list <-
list(confintNormalFn[[i]],
lower_limit=low_values,
estimate=mean_values,
upper_limit=up_values,
size=info_values,
clr.line = clr.line,
clr.marker = clr.marker,
lwd=lwd.ci)
}
# Add additional arguments that are passed on
# from the original parameters
if (length(list(...)) > 0){
ll <- list(...)
for (name in names(ll)){
call_list[[name]] <- ll[[name]]
}
}
# Do the actual drawing of the object
eval(as.call(call_list))
}
upViewport()
}
# Output the legend if it is inside the main plot
if (length(legend) > 0 && is.list(legend.pos)){
plot_vp <- viewport(layout.pos.row = 1:nr,
layout.pos.col = 2 * nc + 1,
name = "main_plot_area")
pushViewport(plot_vp)
if ("align" %in% names(legend.pos) && legend.pos[["align"]] == "horizontal"){
# Calculated with padding above
height <- legend_horizontal_height
# Calculate the horizontal width by iterating througha all elements
# as each element may have a different width
width <- 0
for (i in 1:length(lGrobs)){
if (width > 0){
width <- width + convertUnit(colgap, unitTo="npc", valueOnly=TRUE)
}
width <- width + convertUnit(attr(lGrobs, "max_height") + colgap + attr(lGrobs[[i]], "width"), unitTo="npc", valueOnly=TRUE)
}
# Add the padding
width <- unit(width + convertUnit(legend.padding, unitTo="npc", valueOnly=TRUE)*2, "npc")
}else{
legend_height <- attr(lGrobs, "line_height_and_spacing")[rep(1:2, length.out=length(legend)*2-1)]
if (!is.null(attr(lGrobs, "title"))){
legend_height <- unit.c(attr(lGrobs, "titleHeight"),
attr(lGrobs, "line_height_and_spacing")[2], legend_height)
}
height <- sum(legend.padding, legend_height, legend.padding)
width <- legend_vertical_width
}
pushViewport(viewport(x=legend.pos[["x"]],
y=legend.pos[["y"]],
width=width,
height=height,
just=legend.pos[["just"]]))
# Draw the legend
prFpDrawLegend(lGrobs = lGrobs,
legend.pos = legend.pos,
col = col,
colgap = colgap,
legend.gp = legend.gp,
legend.r = legend.r,
legend.padding = legend.padding,
legendMarkerFn = legendMarkerFn,
...)
upViewport(2)
}
# Go back to the original viewport
seekViewport("forestplot_margins")
upViewport(2)
}
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