R/svyjskm.R
In jinseob2kim/jskm: Kaplan-Meier Plot with 'ggplot2'
Defines functions
svyjskm
Documented in
svyjskm
#' @title Creates a Weighted Kaplan-Meier plot - svykm.object in survey package
#' @description Creates a Weighted Kaplan-Meier plot - svykm.object in survey package
#' @param sfit a svykm object
#' @param xlabs x-axis label, Default: 'Time-to-event'
#' @param ylabs y-axis label.
#' @param xlims numeric: list of min and max for x-axis. Default: NULL
#' @param ylims numeric: list of min and max for y-axis. Default: c(0, 1)
#' @param surv.scale scale transformation of survival curves. Allowed values are "default" or "percent".
#' @param ystratalabs character list. A list of names for each strata. Default: NULL
#' @param ystrataname The legend name. Default: 'Strata'
#' @param timeby numeric: control the granularity along the time-axis; defaults to 7 time-points.
#' @param main plot title, Default: ''
#' @param pval logical: add the pvalue to the plot?, Default: FALSE
#' @param pval.size numeric value specifying the p-value text size. Default is 5.
#' @param pval.coord numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL
#' @param pval.testname logical: add '(Log-rank)' text to p-value. Default = F
#' @param legend logical. should a legend be added to the plot? Default: TRUE
#' @param ci logical. Should confidence intervals be plotted. Default = NULL
#' @param legendposition numeric. x, y position of the legend if plotted. Default: c(0.85, 0.8)
#' @param linecols Character or Character vector. Colour brewer pallettes too colour lines. Default ="Set1", "black" for black with dashed line, character vector for the customization of line colors.
#' @param dashed logical. Should a variety of linetypes be used to identify lines. Default: FALSE
#' @param cumhaz Show cumulaive incidence function, Default: F
#' @param design Data design for reactive design data , Default: NULL
#' @param subs = NULL,
#' @param table logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
#' @param label.nrisk Numbers at risk label. Default = "Numbers at risk"
#' @param size.label.nrisk Font size of label.nrisk. Default = 10
#' @param cut.landmark cut-off for landmark analysis, Default = NULL
#' @param showpercent Shows the percentages on the right side.
#' @param linewidth Line witdh, Default = 0.75
#' @param theme Theme of the plot, Default = NULL, "nejm" for NEJMOA style, "jama" for JAMA style
#' @param nejm.infigure.ratiow Ratio of infigure width to total width, Default = 0.6
#' @param nejm.infigure.ratioh Ratio of infigure height to total height, Default = 0.5
#' @param nejm.infigure.ylim y-axis limit of infigure, Default = c(0,1)
#' @param ... PARAM_DESCRIPTION
#' @return plot
#' @details DETAILS
#' @examples
#' library(survey)
#' data(pbc, package = "survival")
#' pbc$randomized <- with(pbc, !is.na(trt) & trt > 0)
#' biasmodel <- glm(randomized ~ age * edema, data = pbc)
#' pbc$randprob <- fitted(biasmodel)
#' dpbc <- svydesign(id = ~1, prob = ~randprob, strata = ~edema, data = subset(pbc, randomized))
#' s1 <- svykm(Surv(time, status > 0) ~ sex, design = dpbc)
#' svyjskm(s1)
#' @rdname svyjskm
#' @import ggplot2
#' @importFrom stats formula
#' @importFrom survey svyranktest
#' @importFrom survival Surv
#' @importFrom ggpubr ggarrange
#' @importFrom patchwork inset_element
#' @export
svyjskm <- function(sfit,
theme = NULL,
xlabs = "Time-to-event",
ylabs = "Survival probability",
xlims = NULL,
ylims = c(0, 1),
ystratalabs = NULL,
ystrataname = NULL,
surv.scale = c("default", "percent"),
timeby = NULL,
main = "",
pval = FALSE,
pval.size = 5,
pval.coord = c(NULL, NULL),
pval.testname = F,
legend = TRUE,
legendposition = c(0.85, 0.8),
ci = NULL,
linecols = "Set1",
dashed = FALSE,
cumhaz = F,
design = NULL,
subs = NULL,
table = F,
label.nrisk = "Numbers at risk",
size.label.nrisk = 10,
cut.landmark = NULL,
showpercent = F,
linewidth = 0.75,
nejm.infigure.ratiow = 0.6,
nejm.infigure.ratioh = 0.5,
nejm.infigure.ylim = c(0, 1),
...) {
surv <- strata <- lower <- upper <- NULL
if (!is.null(theme) && theme == "nejm") legendposition <- "right"
if (is.null(timeby)) {
if (inherits(sfit, "svykmlist")) {
timeby <- signif(max(sapply(sfit, function(x) {
max(x$time)
})) / 7, 1)
} else if (inherits(sfit, "svykm")) {
timeby <- signif(max(sfit$time) / 7, 1)
}
}
if (is.null(ci)) {
if (inherits(sfit, "svykmlist")) {
ci <- "varlog" %in% names(sfit[[1]])
} else if (inherits(sfit, "svykm")) {
ci <- "varlog" %in% names(sfit)
}
}
if (ci & !is.null(cut.landmark)) {
if (is.null(design)) {
design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
if ("error" %in% class(design)) {
stop("'pval' option requires design object. please input 'design' option")
}
}
var.time <- as.character(formula(sfit)[[2]][[2]])
var.event <- as.character(formula(sfit)[[2]][[3]])
if (length(var.event) > 1) {
var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
var.event <- var.event[sapply(var.event, function(x) {
"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))
})]
}
design1 <- design
design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
sfit2 <- survey::svykm(formula(sfit), design = subset(design, get(var.time) >= cut.landmark), se = T)
}
if (inherits(sfit, "svykmlist")) {
if (is.null(ystrataname)) ystrataname <- as.character(formula(sfit)[[3]])
if (ci) {
if ("varlog" %in% names(sfit[[1]])) {
df <- do.call(rbind, lapply(names(sfit), function(x) {
data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv, "lower" = pmax(0, exp(log(sfit[[x]]$surv) - 1.96 * sqrt(sfit[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit[[x]]$surv) + 1.96 * sqrt(sfit[[x]]$varlog))))
}))
if (!is.null(cut.landmark)) {
df2 <- do.call(rbind, lapply(names(sfit2), function(x) {
data.frame("strata" = x, "time" = sfit2[[x]]$time, "surv" = sfit2[[x]]$surv, "lower" = pmax(0, exp(log(sfit2[[x]]$surv) - 1.96 * sqrt(sfit2[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit2[[x]]$surv) + 1.96 * sqrt(sfit2[[x]]$varlog))))
}))
df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = unique(df$strata), "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
}
} else {
stop("No CI information in svykmlist object. please run svykm with se = T option.")
}
} else {
df <- do.call(rbind, lapply(names(sfit), function(x) {
data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv)
}))
if (!is.null(cut.landmark)) {
for (v in unique(df$strata)) {
if (nrow(subset(df, time == cut.landmark & strata == v)) == 0) {
df <- rbind(df, data.frame(strata = v, time = cut.landmark, surv = 1))
} else {
df[df$time == cut.landmark & df$strata == v, "surv"] <- 1
}
df[df$time > cut.landmark & df$strata == v, "surv"] <- df[df$time > cut.landmark & df$strata == v, "surv"] / min(df[df$time < cut.landmark & df$strata == v, "surv"])
}
}
}
df$strata <- factor(df$strata, levels = names(sfit))
times <- seq(0, max(sapply(sfit, function(x) {
max(x$time)
})), by = timeby)
if (is.null(ystratalabs)) {
ystratalabs <- levels(df$strata)
}
if (is.null(xlims)) {
xlims <- c(0, max(sapply(sfit, function(x) {
max(x$time)
})))
}
} else if (inherits(sfit, "svykm")) {
if (is.null(ystrataname)) ystrataname <- "Strata"
if (ci) {
if ("varlog" %in% names(sfit)) {
df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv, "lower" = pmax(0, exp(log(sfit$surv) - 1.96 * sqrt(sfit$varlog))), "upper" = pmax(0, exp(log(sfit$surv) + 1.96 * sqrt(sfit$varlog))))
if (!is.null(cut.landmark)) {
df2 <- data.frame("strata" = "All", "time" = sfit2$time, "surv" = sfit2$surv, "lower" = pmax(0, exp(log(sfit2$surv) - 1.96 * sqrt(sfit2$varlog))), "upper" = pmax(0, exp(log(sfit2$surv) + 1.96 * sqrt(sfit2$varlog))))
df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = "All", "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
}
} else {
stop("No CI information in svykm object. please run svykm with se = T option.")
}
} else {
df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv)
if (!is.null(cut.landmark)) {
if (nrow(subset(df, time == cut.landmark)) == 0) {
df <- rbind(df, data.frame(strata = "All", time = cut.landmark, surv = 1))
} else {
df[df$time == cut.landmark, "surv"] <- 1
}
df[df$time > cut.landmark, "surv"] <- df[df$time > cut.landmark, "surv"] / min(df[df$time < cut.landmark, "surv"])
}
}
times <- seq(0, max(sfit$time), by = timeby)
if (is.null(ystratalabs)) {
ystratalabs <- "All"
}
if (is.null(xlims)) {
xlims <- c(0, max(sfit$time))
}
}
m <- max(nchar(ystratalabs))
if (cumhaz) {
df$surv <- 1 - df$surv
if (ci) {
upper.new <- 1 - df$lower
lower.new <- 1 - df$upper
df$lower <- lower.new
df$upper <- upper.new
}
}
# Final changes to data for survival plot
levels(df$strata) <- ystratalabs
zeros <- data.frame("strata" = factor(ystratalabs, levels = levels(df$strata)), "time" = 0, "surv" = 1)
if (ci) {
zeros$upper <- 1
zeros$lower <- 1
}
if (cumhaz) {
zeros$surv <- 0
if (ci) {
zeros$lower <- 0
zeros$upper <- 0
}
}
df <- rbind(zeros, df)
d <- length(levels(df$strata))
###################################
# specifying axis parameteres etc #
###################################
if (dashed == TRUE | all(linecols == "black")) {
linetype <- c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash", "1F", "F1", "4C88C488", "12345678")
} else {
linetype <- c("solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid")
}
# Scale transformation
# ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
surv.scale <- match.arg(surv.scale)
scale_labels <- ggplot2::waiver()
if (surv.scale == "percent") scale_labels <- scales::percent
p <- ggplot2::ggplot(df, aes(x = time, y = surv, colour = strata, linetype = strata)) +
ggtitle(main)
linecols2 <- linecols
if (all(linecols == "black")) {
linecols <- "Set1"
p <- ggplot2::ggplot(df, aes(x = time, y = surv, linetype = strata)) +
ggtitle(main)
}
# Set up theme elements
p <- p + theme_bw() +
theme(
axis.title.x = element_text(vjust = 0.7),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, colour = "black"),
legend.position = legendposition,
legend.background = element_rect(fill = NULL),
legend.key = element_rect(colour = NA),
panel.border = element_blank(),
plot.margin = unit(c(0, 1, .5, ifelse(m < 10, 1.5, 2.5)), "lines"),
axis.line.x = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
axis.line.y = element_line(linewidth = 0.5, linetype = "solid", colour = "black")
) +
scale_x_continuous(xlabs, breaks = times, limits = xlims) +
scale_y_continuous(ylabs, limits = ylims, labels = scale_labels)
if (!is.null(theme) && theme == "jama") {
p <- p + theme(
panel.grid.major.x = element_blank()
)
} else {
p <- p + theme(
panel.grid.major = element_blank()
)
}
# Removes the legend:
if (legend == FALSE) {
p <- p + theme(legend.position = "none")
}
# Add lines too plot
if (is.null(cut.landmark)) {
p <- p + geom_step(linewidth = linewidth) +
scale_linetype_manual(name = ystrataname, values = linetype)
} else {
p <- p + geom_step(data = subset(df, time < cut.landmark), linewidth = linewidth) + geom_step(data = subset(df, time >= cut.landmark), linewidth = linewidth) +
scale_linetype_manual(name = ystrataname, values = linetype)
}
brewer.palette <- c(
"BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2",
"Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples",
"RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd"
)
if (!is.null(theme) && theme == "jama") {
col.pal <- c("#00AFBB", "#E7B800", "#FC4E07")
col.pal <- rep(col.pal, ceiling(length(ystratalabs) / 3))
} else if (all(linecols %in% brewer.palette)) {
col.pal <- NULL
} else {
col.pal <- linecols
col.pal <- rep(col.pal, ceiling(length(ystratalabs) / length(linecols)))
}
if (is.null(col.pal)) {
p <- p + scale_colour_brewer(name = ystrataname, palette = linecols)
} else {
p <- p + scale_color_manual(name = ystrataname, values = col.pal)
}
# Add 95% CI to plot
if (ci == TRUE) {
if (all(linecols2 == "black")) {
p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper), alpha = 0.25, colour = NA)
} else if (is.null(col.pal)) {
p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper, fill = strata), alpha = 0.25, colour = NA) + scale_fill_brewer(name = ystrataname, palette = linecols)
} else {
p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper, fill = strata), alpha = 0.25, colour = NA) + scale_fill_manual(name = ystrataname, values = col.pal)
}
}
if (!is.null(cut.landmark)) {
p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
}
p1 <- p
## p-value
if (inherits(sfit, "svykm")) pval <- FALSE
# if(is.null(design)) pval <- FALSE
if (showpercent == TRUE) {
if (is.null(cut.landmark)) {
y.percent <- df[df$time %in% tapply(df$time, df$strata, max), "surv"]
p <- p + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black")
if (!is.null(theme) && theme == "nejm") {
p1 <- p1 + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black", size = nejm.infigure.ratiow * 5)
}
} else {
df.cut <- df[df$time < cut.landmark, ]
y.percent1 <- df.cut[df.cut$time %in% tapply(df.cut$time, df.cut$strata, max), "surv"]
y.percent2 <- df[df$time %in% tapply(df$time, df$strata, max), "surv"]
p <- p + annotate(geom = "text", x = cut.landmark, y = y.percent1, label = paste0(round(100 * y.percent1, 1), "%"), color = "black") +
annotate(geom = "text", x = xlims[2], y = y.percent2, label = paste0(round(100 * y.percent2, 1), "%"), color = "black")
if (!is.null(theme) && theme == "nejm") {
p1 <- p1 + annotate(geom = "text", x = cut.landmark, y = y.percent1, label = paste0(round(100 * y.percent1, 1), "%"), color = "black", size = nejm.infigure.ratiow * 5) +
annotate(geom = "text", x = xlims[2], y = y.percent2, label = paste0(round(100 * y.percent2, 1), "%"), color = "black", size = nejm.infigure.ratiow * 5)
}
}
}
if (pval) {
if (is.null(design)) {
design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
if ("error" %in% class(design)) {
stop("'pval' option requires design object. please input 'design' option")
}
}
if (is.null(cut.landmark)) {
sdiff <- survey::svylogrank(formula(sfit), design = design)
pvalue <- sdiff[[2]][2]
pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
# MOVE P-VALUE LEGEND HERE BELOW [set x and y]
if (is.null(pval.coord)) {
p <- p + annotate("text", x = as.integer(max(sapply(sfit, function(x) {
max(x$time) / 10
}))), y = 0.1 + ylims[1], label = pvaltxt, size = pval.size)
} else {
p <- p + annotate("text", x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size = pval.size)
}
} else {
if (is.null(design)) {
design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
if ("error" %in% class(design)) {
stop("'pval' option requires design object. please input 'design' option")
}
}
var.time <- as.character(formula(sfit)[[2]][[2]])
var.event <- as.character(formula(sfit)[[2]][[3]])
if (length(var.event) > 1) {
var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
var.event <- var.event[sapply(var.event, function(x) {
"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))
})]
}
design1 <- design
design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
sdiff1 <- survey::svylogrank(formula(sfit), design = design1)
sdiff2 <- survey::svylogrank(formula(sfit), design = subset(design, get(var.time) >= cut.landmark))
pvalue <- sapply(list(sdiff1, sdiff2), function(x) {
x[[2]][2]
})
pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
if (is.null(pval.coord)) {
p <- p + annotate("text", x = c(as.integer(max(sapply(sfit, function(x) {
max(x$time) / 10
}))), as.integer(max(sapply(sfit, function(x) {
max(x$time) / 10
}))) + cut.landmark), y = 0.1 + ylims[1], label = pvaltxt, size = pval.size)
} else {
p <- p + annotate("text", x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size = pval.size)
}
}
}
## Create a blank plot for place-holding
blank.pic <- ggplot(df, aes(time, surv)) +
geom_blank() +
theme_void() + ## Remove gray color
theme(
axis.text.x = element_blank(), axis.text.y = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank(),
axis.ticks = element_blank(),
panel.grid.major = element_blank(), panel.border = element_blank()
)
###################################################
# Create table graphic to include at-risk numbers #
###################################################
n.risk <- NULL
if (table == TRUE) {
if (is.null(design)) {
sfit2 <- survival::survfit(formula(sfit), data = get(as.character(attr(sfit, "call")$design))$variables)
} else {
sfit2 <- survival::survfit(formula(sfit), data = design$variables)
}
# times <- seq(0, max(sfit2$time), by = timeby)
if (is.null(subs)) {
if (length(levels(summary(sfit2)$strata)) == 0) {
subs1 <- 1
subs2 <- 1:length(summary(sfit2, censored = T)$time)
subs3 <- 1:length(summary(sfit2, times = times, extend = TRUE)$time)
} else {
subs1 <- 1:length(levels(summary(sfit2)$strata))
subs2 <- 1:length(summary(sfit2, censored = T)$strata)
subs3 <- 1:length(summary(sfit2, times = times, extend = TRUE)$strata)
}
} else {
for (i in 1:length(subs)) {
if (i == 1) {
ssvar <- paste("(?=.*\\b=", subs[i], sep = "")
}
if (i == length(subs)) {
ssvar <- paste(ssvar, "\\b)(?=.*\\b=", subs[i], "\\b)", sep = "")
}
if (!i %in% c(1, length(subs))) {
ssvar <- paste(ssvar, "\\b)(?=.*\\b=", subs[i], sep = "")
}
if (i == 1 & i == length(subs)) {
ssvar <- paste("(?=.*\\b=", subs[i], "\\b)", sep = "")
}
}
subs1 <- which(regexpr(ssvar, levels(summary(sfit2)$strata), perl = T) != -1)
subs2 <- which(regexpr(ssvar, summary(sfit2, censored = T)$strata, perl = T) != -1)
subs3 <- which(regexpr(ssvar, summary(sfit2, times = times, extend = TRUE)$strata, perl = T) != -1)
}
if (!is.null(subs)) pval <- FALSE
if (length(levels(summary(sfit2)$strata)) == 0) {
Factor <- factor(rep("All", length(subs3)))
} else {
Factor <- factor(summary(sfit2, times = times, extend = TRUE)$strata[subs3])
}
risk.data <- data.frame(
strata = Factor,
time = summary(sfit2, times = times, extend = TRUE)$time[subs3],
n.risk = summary(sfit2, times = times, extend = TRUE)$n.risk[subs3]
)
risk.data$strata <- factor(risk.data$strata, levels = rev(levels(risk.data$strata)))
data.table <- ggplot(risk.data, aes(x = time, y = strata, label = format(n.risk, nsmall = 0))) +
geom_text(size = 3.5) +
theme_bw() +
scale_y_discrete(
breaks = as.character(levels(risk.data$strata)),
labels = rev(ystratalabs)
) +
scale_x_continuous(label.nrisk, limits = xlims) +
theme(
axis.title.x = element_text(size = size.label.nrisk, vjust = 1),
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.border = element_blank(), axis.text.x = element_blank(),
axis.ticks = element_blank(), axis.text.y = element_text(face = "bold", hjust = 1)
)
data.table <- data.table +
theme(legend.position = "none") + xlab(NULL) + ylab(NULL)
# ADJUST POSITION OF TABLE FOR AT RISK
data.table <- data.table +
theme(plot.margin = unit(c(-1.5, 1, 0.1, ifelse(m < 10, 3.1, 4.3) - 0.38 * m), "lines"))
}
#######################
# Plotting the graphs #
#######################
if (!is.null(theme) && theme == "nejm") {
p2 <- p1 + coord_cartesian(ylim = nejm.infigure.ylim) + theme(
legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank(),
axis.text = element_text(size = 10 * nejm.infigure.ratiow)
)
p <- p + patchwork::inset_element(p2, 1 - nejm.infigure.ratiow, 1 - nejm.infigure.ratioh, 1, 1, align_to = "panel")
}
if (table == TRUE) {
ggpubr::ggarrange(p, blank.pic, data.table,
nrow = 3,
# align = "v",
heights = c(2, .1, .25)
)
} else {
p
}
}
jinseob2kim/jskm documentation built on April 16, 2024, 6:39 a.m.
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Defines functions svyjskm
Documented in svyjskm
#' @title Creates a Weighted Kaplan-Meier plot - svykm.object in survey package
#' @description Creates a Weighted Kaplan-Meier plot - svykm.object in survey package
#' @param sfit a svykm object
#' @param xlabs x-axis label, Default: 'Time-to-event'
#' @param ylabs y-axis label.
#' @param xlims numeric: list of min and max for x-axis. Default: NULL
#' @param ylims numeric: list of min and max for y-axis. Default: c(0, 1)
#' @param surv.scale scale transformation of survival curves. Allowed values are "default" or "percent".
#' @param ystratalabs character list. A list of names for each strata. Default: NULL
#' @param ystrataname The legend name. Default: 'Strata'
#' @param timeby numeric: control the granularity along the time-axis; defaults to 7 time-points.
#' @param main plot title, Default: ''
#' @param pval logical: add the pvalue to the plot?, Default: FALSE
#' @param pval.size numeric value specifying the p-value text size. Default is 5.
#' @param pval.coord numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL
#' @param pval.testname logical: add '(Log-rank)' text to p-value. Default = F
#' @param legend logical. should a legend be added to the plot? Default: TRUE
#' @param ci logical. Should confidence intervals be plotted. Default = NULL
#' @param legendposition numeric. x, y position of the legend if plotted. Default: c(0.85, 0.8)
#' @param linecols Character or Character vector. Colour brewer pallettes too colour lines. Default ="Set1", "black" for black with dashed line, character vector for the customization of line colors.
#' @param dashed logical. Should a variety of linetypes be used to identify lines. Default: FALSE
#' @param cumhaz Show cumulaive incidence function, Default: F
#' @param design Data design for reactive design data , Default: NULL
#' @param subs = NULL,
#' @param table logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
#' @param label.nrisk Numbers at risk label. Default = "Numbers at risk"
#' @param size.label.nrisk Font size of label.nrisk. Default = 10
#' @param cut.landmark cut-off for landmark analysis, Default = NULL
#' @param showpercent Shows the percentages on the right side.
#' @param linewidth Line witdh, Default = 0.75
#' @param theme Theme of the plot, Default = NULL, "nejm" for NEJMOA style, "jama" for JAMA style
#' @param nejm.infigure.ratiow Ratio of infigure width to total width, Default = 0.6
#' @param nejm.infigure.ratioh Ratio of infigure height to total height, Default = 0.5
#' @param nejm.infigure.ylim y-axis limit of infigure, Default = c(0,1)
#' @param ... PARAM_DESCRIPTION
#' @return plot
#' @details DETAILS
#' @examples
#' library(survey)
#' data(pbc, package = "survival")
#' pbc$randomized <- with(pbc, !is.na(trt) & trt > 0)
#' biasmodel <- glm(randomized ~ age * edema, data = pbc)
#' pbc$randprob <- fitted(biasmodel)
#' dpbc <- svydesign(id = ~1, prob = ~randprob, strata = ~edema, data = subset(pbc, randomized))
#' s1 <- svykm(Surv(time, status > 0) ~ sex, design = dpbc)
#' svyjskm(s1)
#' @rdname svyjskm
#' @import ggplot2
#' @importFrom stats formula
#' @importFrom survey svyranktest
#' @importFrom survival Surv
#' @importFrom ggpubr ggarrange
#' @importFrom patchwork inset_element
#' @export
svyjskm <- function(sfit,
theme = NULL,
xlabs = "Time-to-event",
ylabs = "Survival probability",
xlims = NULL,
ylims = c(0, 1),
ystratalabs = NULL,
ystrataname = NULL,
surv.scale = c("default", "percent"),
timeby = NULL,
main = "",
pval = FALSE,
pval.size = 5,
pval.coord = c(NULL, NULL),
pval.testname = F,
legend = TRUE,
legendposition = c(0.85, 0.8),
ci = NULL,
linecols = "Set1",
dashed = FALSE,
cumhaz = F,
design = NULL,
subs = NULL,
table = F,
label.nrisk = "Numbers at risk",
size.label.nrisk = 10,
cut.landmark = NULL,
showpercent = F,
linewidth = 0.75,
nejm.infigure.ratiow = 0.6,
nejm.infigure.ratioh = 0.5,
nejm.infigure.ylim = c(0, 1),
...) {
surv <- strata <- lower <- upper <- NULL
if (!is.null(theme) && theme == "nejm") legendposition <- "right"
if (is.null(timeby)) {
if (inherits(sfit, "svykmlist")) {
timeby <- signif(max(sapply(sfit, function(x) {
max(x$time)
})) / 7, 1)
} else if (inherits(sfit, "svykm")) {
timeby <- signif(max(sfit$time) / 7, 1)
}
}
if (is.null(ci)) {
if (inherits(sfit, "svykmlist")) {
ci <- "varlog" %in% names(sfit[[1]])
} else if (inherits(sfit, "svykm")) {
ci <- "varlog" %in% names(sfit)
}
}
if (ci & !is.null(cut.landmark)) {
if (is.null(design)) {
design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
if ("error" %in% class(design)) {
stop("'pval' option requires design object. please input 'design' option")
}
}
var.time <- as.character(formula(sfit)[[2]][[2]])
var.event <- as.character(formula(sfit)[[2]][[3]])
if (length(var.event) > 1) {
var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
var.event <- var.event[sapply(var.event, function(x) {
"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))
})]
}
design1 <- design
design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
sfit2 <- survey::svykm(formula(sfit), design = subset(design, get(var.time) >= cut.landmark), se = T)
}
if (inherits(sfit, "svykmlist")) {
if (is.null(ystrataname)) ystrataname <- as.character(formula(sfit)[[3]])
if (ci) {
if ("varlog" %in% names(sfit[[1]])) {
df <- do.call(rbind, lapply(names(sfit), function(x) {
data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv, "lower" = pmax(0, exp(log(sfit[[x]]$surv) - 1.96 * sqrt(sfit[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit[[x]]$surv) + 1.96 * sqrt(sfit[[x]]$varlog))))
}))
if (!is.null(cut.landmark)) {
df2 <- do.call(rbind, lapply(names(sfit2), function(x) {
data.frame("strata" = x, "time" = sfit2[[x]]$time, "surv" = sfit2[[x]]$surv, "lower" = pmax(0, exp(log(sfit2[[x]]$surv) - 1.96 * sqrt(sfit2[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit2[[x]]$surv) + 1.96 * sqrt(sfit2[[x]]$varlog))))
}))
df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = unique(df$strata), "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
}
} else {
stop("No CI information in svykmlist object. please run svykm with se = T option.")
}
} else {
df <- do.call(rbind, lapply(names(sfit), function(x) {
data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv)
}))
if (!is.null(cut.landmark)) {
for (v in unique(df$strata)) {
if (nrow(subset(df, time == cut.landmark & strata == v)) == 0) {
df <- rbind(df, data.frame(strata = v, time = cut.landmark, surv = 1))
} else {
df[df$time == cut.landmark & df$strata == v, "surv"] <- 1
}
df[df$time > cut.landmark & df$strata == v, "surv"] <- df[df$time > cut.landmark & df$strata == v, "surv"] / min(df[df$time < cut.landmark & df$strata == v, "surv"])
}
}
}
df$strata <- factor(df$strata, levels = names(sfit))
times <- seq(0, max(sapply(sfit, function(x) {
max(x$time)
})), by = timeby)
if (is.null(ystratalabs)) {
ystratalabs <- levels(df$strata)
}
if (is.null(xlims)) {
xlims <- c(0, max(sapply(sfit, function(x) {
max(x$time)
})))
}
} else if (inherits(sfit, "svykm")) {
if (is.null(ystrataname)) ystrataname <- "Strata"
if (ci) {
if ("varlog" %in% names(sfit)) {
df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv, "lower" = pmax(0, exp(log(sfit$surv) - 1.96 * sqrt(sfit$varlog))), "upper" = pmax(0, exp(log(sfit$surv) + 1.96 * sqrt(sfit$varlog))))
if (!is.null(cut.landmark)) {
df2 <- data.frame("strata" = "All", "time" = sfit2$time, "surv" = sfit2$surv, "lower" = pmax(0, exp(log(sfit2$surv) - 1.96 * sqrt(sfit2$varlog))), "upper" = pmax(0, exp(log(sfit2$surv) + 1.96 * sqrt(sfit2$varlog))))
df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = "All", "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
}
} else {
stop("No CI information in svykm object. please run svykm with se = T option.")
}
} else {
df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv)
if (!is.null(cut.landmark)) {
if (nrow(subset(df, time == cut.landmark)) == 0) {
df <- rbind(df, data.frame(strata = "All", time = cut.landmark, surv = 1))
} else {
df[df$time == cut.landmark, "surv"] <- 1
}
df[df$time > cut.landmark, "surv"] <- df[df$time > cut.landmark, "surv"] / min(df[df$time < cut.landmark, "surv"])
}
}
times <- seq(0, max(sfit$time), by = timeby)
if (is.null(ystratalabs)) {
ystratalabs <- "All"
}
if (is.null(xlims)) {
xlims <- c(0, max(sfit$time))
}
}
m <- max(nchar(ystratalabs))
if (cumhaz) {
df$surv <- 1 - df$surv
if (ci) {
upper.new <- 1 - df$lower
lower.new <- 1 - df$upper
df$lower <- lower.new
df$upper <- upper.new
}
}
# Final changes to data for survival plot
levels(df$strata) <- ystratalabs
zeros <- data.frame("strata" = factor(ystratalabs, levels = levels(df$strata)), "time" = 0, "surv" = 1)
if (ci) {
zeros$upper <- 1
zeros$lower <- 1
}
if (cumhaz) {
zeros$surv <- 0
if (ci) {
zeros$lower <- 0
zeros$upper <- 0
}
}
df <- rbind(zeros, df)
d <- length(levels(df$strata))
###################################
# specifying axis parameteres etc #
###################################
if (dashed == TRUE | all(linecols == "black")) {
linetype <- c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash", "1F", "F1", "4C88C488", "12345678")
} else {
linetype <- c("solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid", "solid")
}
# Scale transformation
# ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
surv.scale <- match.arg(surv.scale)
scale_labels <- ggplot2::waiver()
if (surv.scale == "percent") scale_labels <- scales::percent
p <- ggplot2::ggplot(df, aes(x = time, y = surv, colour = strata, linetype = strata)) +
ggtitle(main)
linecols2 <- linecols
if (all(linecols == "black")) {
linecols <- "Set1"
p <- ggplot2::ggplot(df, aes(x = time, y = surv, linetype = strata)) +
ggtitle(main)
}
# Set up theme elements
p <- p + theme_bw() +
theme(
axis.title.x = element_text(vjust = 0.7),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, colour = "black"),
legend.position = legendposition,
legend.background = element_rect(fill = NULL),
legend.key = element_rect(colour = NA),
panel.border = element_blank(),
plot.margin = unit(c(0, 1, .5, ifelse(m < 10, 1.5, 2.5)), "lines"),
axis.line.x = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
axis.line.y = element_line(linewidth = 0.5, linetype = "solid", colour = "black")
) +
scale_x_continuous(xlabs, breaks = times, limits = xlims) +
scale_y_continuous(ylabs, limits = ylims, labels = scale_labels)
if (!is.null(theme) && theme == "jama") {
p <- p + theme(
panel.grid.major.x = element_blank()
)
} else {
p <- p + theme(
panel.grid.major = element_blank()
)
}
# Removes the legend:
if (legend == FALSE) {
p <- p + theme(legend.position = "none")
}
# Add lines too plot
if (is.null(cut.landmark)) {
p <- p + geom_step(linewidth = linewidth) +
scale_linetype_manual(name = ystrataname, values = linetype)
} else {
p <- p + geom_step(data = subset(df, time < cut.landmark), linewidth = linewidth) + geom_step(data = subset(df, time >= cut.landmark), linewidth = linewidth) +
scale_linetype_manual(name = ystrataname, values = linetype)
}
brewer.palette <- c(
"BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2",
"Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples",
"RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd"
)
if (!is.null(theme) && theme == "jama") {
col.pal <- c("#00AFBB", "#E7B800", "#FC4E07")
col.pal <- rep(col.pal, ceiling(length(ystratalabs) / 3))
} else if (all(linecols %in% brewer.palette)) {
col.pal <- NULL
} else {
col.pal <- linecols
col.pal <- rep(col.pal, ceiling(length(ystratalabs) / length(linecols)))
}
if (is.null(col.pal)) {
p <- p + scale_colour_brewer(name = ystrataname, palette = linecols)
} else {
p <- p + scale_color_manual(name = ystrataname, values = col.pal)
}
# Add 95% CI to plot
if (ci == TRUE) {
if (all(linecols2 == "black")) {
p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper), alpha = 0.25, colour = NA)
} else if (is.null(col.pal)) {
p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper, fill = strata), alpha = 0.25, colour = NA) + scale_fill_brewer(name = ystrataname, palette = linecols)
} else {
p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper, fill = strata), alpha = 0.25, colour = NA) + scale_fill_manual(name = ystrataname, values = col.pal)
}
}
if (!is.null(cut.landmark)) {
p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
}
p1 <- p
## p-value
if (inherits(sfit, "svykm")) pval <- FALSE
# if(is.null(design)) pval <- FALSE
if (showpercent == TRUE) {
if (is.null(cut.landmark)) {
y.percent <- df[df$time %in% tapply(df$time, df$strata, max), "surv"]
p <- p + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black")
if (!is.null(theme) && theme == "nejm") {
p1 <- p1 + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black", size = nejm.infigure.ratiow * 5)
}
} else {
df.cut <- df[df$time < cut.landmark, ]
y.percent1 <- df.cut[df.cut$time %in% tapply(df.cut$time, df.cut$strata, max), "surv"]
y.percent2 <- df[df$time %in% tapply(df$time, df$strata, max), "surv"]
p <- p + annotate(geom = "text", x = cut.landmark, y = y.percent1, label = paste0(round(100 * y.percent1, 1), "%"), color = "black") +
annotate(geom = "text", x = xlims[2], y = y.percent2, label = paste0(round(100 * y.percent2, 1), "%"), color = "black")
if (!is.null(theme) && theme == "nejm") {
p1 <- p1 + annotate(geom = "text", x = cut.landmark, y = y.percent1, label = paste0(round(100 * y.percent1, 1), "%"), color = "black", size = nejm.infigure.ratiow * 5) +
annotate(geom = "text", x = xlims[2], y = y.percent2, label = paste0(round(100 * y.percent2, 1), "%"), color = "black", size = nejm.infigure.ratiow * 5)
}
}
}
if (pval) {
if (is.null(design)) {
design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
if ("error" %in% class(design)) {
stop("'pval' option requires design object. please input 'design' option")
}
}
if (is.null(cut.landmark)) {
sdiff <- survey::svylogrank(formula(sfit), design = design)
pvalue <- sdiff[[2]][2]
pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
# MOVE P-VALUE LEGEND HERE BELOW [set x and y]
if (is.null(pval.coord)) {
p <- p + annotate("text", x = as.integer(max(sapply(sfit, function(x) {
max(x$time) / 10
}))), y = 0.1 + ylims[1], label = pvaltxt, size = pval.size)
} else {
p <- p + annotate("text", x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size = pval.size)
}
} else {
if (is.null(design)) {
design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
if ("error" %in% class(design)) {
stop("'pval' option requires design object. please input 'design' option")
}
}
var.time <- as.character(formula(sfit)[[2]][[2]])
var.event <- as.character(formula(sfit)[[2]][[3]])
if (length(var.event) > 1) {
var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
var.event <- var.event[sapply(var.event, function(x) {
"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))
})]
}
design1 <- design
design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
sdiff1 <- survey::svylogrank(formula(sfit), design = design1)
sdiff2 <- survey::svylogrank(formula(sfit), design = subset(design, get(var.time) >= cut.landmark))
pvalue <- sapply(list(sdiff1, sdiff2), function(x) {
x[[2]][2]
})
pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
if (is.null(pval.coord)) {
p <- p + annotate("text", x = c(as.integer(max(sapply(sfit, function(x) {
max(x$time) / 10
}))), as.integer(max(sapply(sfit, function(x) {
max(x$time) / 10
}))) + cut.landmark), y = 0.1 + ylims[1], label = pvaltxt, size = pval.size)
} else {
p <- p + annotate("text", x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size = pval.size)
}
}
}
## Create a blank plot for place-holding
blank.pic <- ggplot(df, aes(time, surv)) +
geom_blank() +
theme_void() + ## Remove gray color
theme(
axis.text.x = element_blank(), axis.text.y = element_blank(),
axis.title.x = element_blank(), axis.title.y = element_blank(),
axis.ticks = element_blank(),
panel.grid.major = element_blank(), panel.border = element_blank()
)
###################################################
# Create table graphic to include at-risk numbers #
###################################################
n.risk <- NULL
if (table == TRUE) {
if (is.null(design)) {
sfit2 <- survival::survfit(formula(sfit), data = get(as.character(attr(sfit, "call")$design))$variables)
} else {
sfit2 <- survival::survfit(formula(sfit), data = design$variables)
}
# times <- seq(0, max(sfit2$time), by = timeby)
if (is.null(subs)) {
if (length(levels(summary(sfit2)$strata)) == 0) {
subs1 <- 1
subs2 <- 1:length(summary(sfit2, censored = T)$time)
subs3 <- 1:length(summary(sfit2, times = times, extend = TRUE)$time)
} else {
subs1 <- 1:length(levels(summary(sfit2)$strata))
subs2 <- 1:length(summary(sfit2, censored = T)$strata)
subs3 <- 1:length(summary(sfit2, times = times, extend = TRUE)$strata)
}
} else {
for (i in 1:length(subs)) {
if (i == 1) {
ssvar <- paste("(?=.*\\b=", subs[i], sep = "")
}
if (i == length(subs)) {
ssvar <- paste(ssvar, "\\b)(?=.*\\b=", subs[i], "\\b)", sep = "")
}
if (!i %in% c(1, length(subs))) {
ssvar <- paste(ssvar, "\\b)(?=.*\\b=", subs[i], sep = "")
}
if (i == 1 & i == length(subs)) {
ssvar <- paste("(?=.*\\b=", subs[i], "\\b)", sep = "")
}
}
subs1 <- which(regexpr(ssvar, levels(summary(sfit2)$strata), perl = T) != -1)
subs2 <- which(regexpr(ssvar, summary(sfit2, censored = T)$strata, perl = T) != -1)
subs3 <- which(regexpr(ssvar, summary(sfit2, times = times, extend = TRUE)$strata, perl = T) != -1)
}
if (!is.null(subs)) pval <- FALSE
if (length(levels(summary(sfit2)$strata)) == 0) {
Factor <- factor(rep("All", length(subs3)))
} else {
Factor <- factor(summary(sfit2, times = times, extend = TRUE)$strata[subs3])
}
risk.data <- data.frame(
strata = Factor,
time = summary(sfit2, times = times, extend = TRUE)$time[subs3],
n.risk = summary(sfit2, times = times, extend = TRUE)$n.risk[subs3]
)
risk.data$strata <- factor(risk.data$strata, levels = rev(levels(risk.data$strata)))
data.table <- ggplot(risk.data, aes(x = time, y = strata, label = format(n.risk, nsmall = 0))) +
geom_text(size = 3.5) +
theme_bw() +
scale_y_discrete(
breaks = as.character(levels(risk.data$strata)),
labels = rev(ystratalabs)
) +
scale_x_continuous(label.nrisk, limits = xlims) +
theme(
axis.title.x = element_text(size = size.label.nrisk, vjust = 1),
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.border = element_blank(), axis.text.x = element_blank(),
axis.ticks = element_blank(), axis.text.y = element_text(face = "bold", hjust = 1)
)
data.table <- data.table +
theme(legend.position = "none") + xlab(NULL) + ylab(NULL)
# ADJUST POSITION OF TABLE FOR AT RISK
data.table <- data.table +
theme(plot.margin = unit(c(-1.5, 1, 0.1, ifelse(m < 10, 3.1, 4.3) - 0.38 * m), "lines"))
}
#######################
# Plotting the graphs #
#######################
if (!is.null(theme) && theme == "nejm") {
p2 <- p1 + coord_cartesian(ylim = nejm.infigure.ylim) + theme(
legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank(),
axis.text = element_text(size = 10 * nejm.infigure.ratiow)
)
p <- p + patchwork::inset_element(p2, 1 - nejm.infigure.ratiow, 1 - nejm.infigure.ratioh, 1, 1, align_to = "panel")
}
if (table == TRUE) {
ggpubr::ggarrange(p, blank.pic, data.table,
nrow = 3,
# align = "v",
heights = c(2, .1, .25)
)
} else {
p
}
}
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