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Risk table alignment modifications - possible fix for #302 and #448 #645

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Risk table alignment modifications - possible fix for #302 and #448 #645

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28 changes: 22 additions & 6 deletions R/ggsurvplot_core.R
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Original file line number Diff line number Diff line change
Expand Up @@ -170,6 +170,7 @@ ggsurvplot_core <- function(fit, data = NULL, fun = NULL,
pms$y.text.col <- risk.table.y.text.col
pms$fontsize <- risk.table.fontsize
pms$survtable <- "risk.table"
pms$risk.table.pos <- risk.table.pos
# color risk.table ticks by strata
if(risk.table.y.text.col) pms$y.text.col <- scurve_cols
res$table <- risktable <- do.call(ggsurvtable, pms)
Expand Down Expand Up @@ -241,6 +242,10 @@ ggsurvplot_core <- function(fit, data = NULL, fun = NULL,
cumevents = cumevents.y.text.col,
cumcensor = cumcensor.y.text.col
)
x.axis.limits <- list(
x.axis.min = xlim[1],
x.axis.max = xlim[2]
)

# Returning the data used to generate the survival plots
res$data.survplot <- d
Expand All @@ -255,6 +260,7 @@ ggsurvplot_core <- function(fit, data = NULL, fun = NULL,
attr(res, "cumcensor") <- cumcensor
attr(res, "risk.table.pos") <- risk.table.pos
attr(res, "axes.offset") <- axes.offset
attr(res, "x.axis.limits") <- x.axis.limits
res
}

Expand Down Expand Up @@ -462,14 +468,24 @@ ggsurvplot_core <- function(fit, data = NULL, fun = NULL,
.time <- survplot$data$time
ymax <- nstrata*0.05
ymin <- -0.05
xmin <- -max(.time)/20

if(!axes.offset){
ymin <- -0.02
xmin <- -max(.time)/50
x.axis.limits <- attr(ggsurv, "x.axis.limits")
xlim.lower <- x.axis.limits$x.axis.min
xlim.upper <- x.axis.limits$x.axis.max
expansion.lower <- (xlim.upper-xlim.lower)*0.05
expansion.upper <- (xlim.upper-xlim.lower)*0.05

if (axes.offset) {
xmin <- xlim.lower-expansion.lower
xmax <- xlim.upper+expansion.upper
}
else if(!axes.offset){
ymin <- 0
ymax <- nstrata*0.06
xmin <- xlim.lower
xmax <- xlim.upper
}
risktable_grob = ggplotGrob(risktable)
survplot <- survplot + annotation_custom(grob = risktable_grob, xmin = xmin,
survplot <- survplot + annotation_custom(grob = risktable_grob, xmin = xmin, xmax = xmax,
ymin = ymin, ymax = ymax)
ggsurv$plot <- survplot
ggsurv$table <- NULL
Expand Down
23 changes: 20 additions & 3 deletions R/ggsurvtable.R
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,7 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso
# Helper function to plot a specific survival table
.plot_survtable <- function (survsummary, times, survtable = c("cumevents", "risk.table", "cumcensor"),
risk.table.type = c("absolute", "percentage", "abs_pct", "nrisk_cumcensor", "nrisk_cumevents"),
risk.table.pos = risk.table.pos,
color = "black", palette = NULL, xlim = NULL,
xscale = 1,
title = NULL, xlab = "Time", ylab = "Strata",
Expand All @@ -193,6 +194,7 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso

survtable <- match.arg(survtable)
risk.table.type <- match.arg(risk.table.type)
risk.table.pos <- match.arg(risk.table.pos)

# Defining plot title
#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Expand Down Expand Up @@ -280,20 +282,24 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso
# Plotting survival table
#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
.expand <- ggplot2::waiver()
# Tables labels Offset from origing
# Set first risk table value offset from origin and set y-axis margin size
risktable.ytick.rmargin <- 0
if(!axes.offset){
.expand <- c(0,0)
offset <- max(xlim)/30
offset <- 0
survsummary <- survsummary %>%
dplyr::mutate(time = ifelse(time == 0, offset, time))

if (risk.table.pos=="out")
risktable.ytick.rmargin <- 15
}

p <- ggplot(survsummary, mapping) +
scale_shape_manual(values = 1:length(levels(survsummary$strata)))+
ggpubr::geom_exec(geom_text, data = survsummary, size = fontsize, color = color, family = font.family) +
ggtheme +
scale_y_discrete(breaks = as.character(levels(survsummary$strata)),labels = yticklabs ) +
coord_cartesian(xlim = xlim) +
coord_cartesian(xlim = xlim, clip='off') +
labs(title = title, x = xlab, y = ylab, color = legend.title, shape = legend.title)

if (survtable == "risk.table")
Expand All @@ -309,6 +315,17 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso
trans = "log10", labels = xticklabels)

p <- p + tables.theme

# Apply y-axis margin and prevent lines being drawn on first risk table value
if (risk.table.pos=="out" & !axes.offset) {
p <- p +
theme(
axis.text.y = element_text(hjust = 0, margin = margin(r=risktable.ytick.rmargin)),
axis.ticks.y = element_blank(),
axis.line.y = element_blank(),
panel.border = element_blank()
)
}

if(!y.text) {
p <- .set_large_dash_as_ytext(p)
Expand Down