问题
I'm trying to make a simple shiny ap for creating kaplan-meier survival curves that are stratified by selection the user makes. When I code the KM calculation statically (with the column name thorTr) it works but the calculation and plot is static. When I replace with input$s I get ERROR:variable lengths differ (found for 'input$s')
I've tried looking at other code which use as.formula and paste, but I don't understand and couldn't get to work. But I am a new R and Shiny user so maybe I didn't get it right. Here is a similar shiny ap but I want to use survminer and the ggsurvplot for plotting
library(shiny)
library(ggplot2)
library(survival)
library(survminer)
#load data
data(GBSG2, package = "TH.data")
#Define UI for application that plots stratified km curves
ui <- fluidPage(
# Sidebar layout with a input and output definitions
sidebarLayout(
# Inputs
sidebarPanel(
# Select variable strat
selectInput(inputId = "s",
label = "Select Stratification Variable:",
choices = c("horTh","menostat","tgrade"),
selected = "horTh")
),
# Outputs
mainPanel(
plotOutput(outputId = "km")
)
)
)
# Define server function required to create the km plot
server <- function(input, output) {
# Create the km plot object the plotOutput function is expecting
output$km <- renderPlot({
#calc KM estimate with a hard coded variables - the following line works but obviously is not reactive
#km <- survfit(Surv(time,cens) ~ horTh,data=GBSG2)
#replaced hard coded horTh selection with the respnse from the selection and I get an error
km <- survfit(Surv(time,cens) ~ input$s ,data=GBSG2)
#plot km
ggsurvplot(km)
})
}
# Create a Shiny app object
shinyApp(ui = ui, server = server)
I expect to have a plot that updates the stratification variable with the users selection
回答1:
Two things:
- The formula in the call to
survfit()
needs to be defined explicitly. The object being passed tosurvfit()
in the original code uses a character value on the right hand side of the function. This throws an error, which we can address by translating the entire pasted value into a formula, i.e.,as.formula(paste('Surv(time,cens) ~',input$s))
- The formula needs to be defined in the call to
ggsurvplot()
to avoid scoping issues. This is a little more technical and has to do with the way thatggsurvplot()
is programmed. Basically,ggsurvplot()
can't access a formula that is defined outside of its own call.
Try replacing
km <- survfit(Surv(time,cens) ~ input$s ,data=GBSG2)
ggsurvplot(km)
with
ggsurvplot(survfit(as.formula(paste('Surv(time,cens) ~',input$s)),data=GBSG2))
回答2:
Hi finally got this to work combinigng both solutions. I don't understand the fix but at least it now works the way I wanted it to :)
library(shiny)
library(ggplot2)
library(survival)
library(survminer)
data(GBSG2, package = "TH.data")
# Define UI for application that plots features of movies
ui <- fluidPage(
# Sidebar layout with a input and output definitions
sidebarLayout(
# Inputs
sidebarPanel(
# Select variable strat
selectInput(inputId = "s",
label = "Select Stratification Variable:",
choices = c("Hormone Therapy" = "horTh",
"Menopausal Status" = "menostat",
"Tumor Grade" = "tgrade"),
selected = "horTh")
),
# Outputs
mainPanel(
plotOutput(outputId = "km")
)
)
)
# Define server function required to create the scatterplot
server <- function(input, output) {
# Create the km plot object the plotOutput function is expecting
output$km <- renderPlot({
## calc survival curve and plot
kmdata <- surv_fit(as.formula(paste('Surv(time,cens) ~',input$s)),data=GBSG2)
ggsurvplot(kmdata)
})
}
# Create a Shiny app object
shinyApp(ui = ui, server = server)
回答3:
Try using surv_fit()
instead of survfit()
.
surv_fit()
is a helper from survminer
which does different scoping compared to survival:survit()
, which is what you seem to need, as Byron suggests.
My snippet looks like:
output$plot <- renderPlot({
formula_text <- paste0("Surv(OS, OS_CENSOR) ~ ", input$covariate)
## for ggsurvplot, use survminer::surv_fit instead of survival:survfit
fit <- surv_fit(as.formula(formula_text), data=os_df)
ggsurvplot(fit = fit, data=os_df)
})
来源:https://stackoverflow.com/questions/54058769/how-to-fix-error-variable-lengths-differ-found-for-inputs-in-r-shiny