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Update for sensitive cases #637

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Update for sensitive cases #637

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dc575fe
Update ggsurvtable.R
jwallib Dec 19, 2023
adcf9e6
Update ggsurvplot_core.R
jwallib Dec 19, 2023
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1 change: 1 addition & 0 deletions R/ggsurvplot_core.R
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,7 @@ ggsurvplot_core <- function(fit, data = NULL, fun = NULL,
pms <- attr(p, "parameters")
surv.color <- pms$color

pms = c(pms,list(...))
pms$fit <- fit
pms$data <- data
pms$risk.table.type <- risk.table.type
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7 changes: 6 additions & 1 deletion R/ggsurvtable.R
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Expand Up @@ -33,6 +33,8 @@ NULL
#' labels will be colored by strata.
#'@param fontsize text font size.
#'@param font.family character vector specifying text element font family, e.g.: font.family = "Courier New".
#'@param obscure.less.than numeric, obscure numbers smaller than this.
#'@param obscure.zero logical, obscure or keep zero.
#'@param ... other arguments passed to the function \code{\link{ggsurvtable}} and \code{\link[ggpubr]{ggpar}}.
#'@return a ggplot.
#'@author Alboukadel Kassambara, \email{alboukadel.kassambara@@gmail.com}
Expand Down Expand Up @@ -188,6 +190,7 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso
font.family = "",
axes.offset = TRUE,
ggtheme = theme_survminer(), tables.theme = ggtheme,
obscure.less.than = -1, obscure.zero = FALSE,
...)
{

Expand Down Expand Up @@ -254,11 +257,12 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso
if(survtable == "cumevents"){
mapping <- aes(x = time, y = rev(strata),
label = cum.n.event, shape = rev(strata))
survsummary$cum.n.event[survsummary$cum.n.event<obscure.less.than & (survsummary$cum.n.event>0 | obscure.zero)] <- paste0('<',obscure.less.than)
}
else if (survtable == "cumcensor"){
mapping <- aes(x = time, y = rev(strata),
label = cum.n.censor, shape = rev(strata))

survsummary$cum.n.event[survsummary$cum.n.censor<obscure.less.than & (survsummary$cum.n.censor>0 | obscure.zero)] <- paste0('<',obscure.less.than)
}
else if (survtable == "risk.table"){
# risk table labels depending on the type argument
Expand All @@ -270,6 +274,7 @@ ggsurvtable <- function (fit, data = NULL, survtable = c("cumevents", "cumcenso
nrisk_cumevents = paste0(survsummary$n.risk, " (", survsummary$cum.n.event, ")"),
survsummary$n.risk
)
llabels[llabels<obscure.less.than & (llabels>0 | obscure.zero)] <- paste0('<',obscure.less.than)
survsummary$llabels <- llabels
mapping <- aes(x = time, y = rev(strata),
label = llabels, shape = rev(strata))
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