rggplot2shinysurvival
Issue with R Shiny App --> Interactive Survival Plots
I am new to R Shiny and I am trying to build a Shiny Web App that produces a survival plot with two reactive inputs. The first input is the study (total=4). The second input is the groups (total=19) to compare survival curves. Ideally, these two inputs would allow me to see in a particular study, how group X survival curve compares to the survival curve of all other groups.
Here is a sample of my data:
ObsNum UniqueID Time Censored Group Group2 Study
1 523B95015 27 1 1 523 1
2 523B95014 27 1 1 523 1
3 523B85051 27 1 1 523 1
4 523B95009 27 1 1 523 1
5 523B85048 27 1 1 523 1
6 523B85050 27 1 1 523 1
7 675B89002 27 1 8 675 1
8 556B95006 27 1 12 556 1
9 556B85030 27 1 12 556 1
10 556B85044 27 1 12 556 1
11 556B95035 27 1 12 556 1
12 556B95000 27 1 12 556 1
13 556B95004 27 1 12 556 1
14 556B95002 27 1 12 556 1
15 756Y81172 27 1 17 756 1
16 741B95022 27 1 99 741 1
17 741B95020 27 1 99 741 1
18 619B92008 28 1 7 619 1
19 552B89003 28 1 10 552 1
20 101B94097 28 1 99 101 1
21 101B94098 28 1 99 101 1
22 618C84582 29 1 23 618 1
23 618C84580 29 1 23 618 1
24 618C84581 29 1 23 618 1
25 730B90003 29 1 99 730 1
26 646B42015 34 1 4 646 1
27 671B60009 35 1 17 671 1
28 612C80247 35 1 21 612 1
29 700C64500 35 1 99 791 1
30 101B89052 40 1 99 101 1
31 101B85047 40 1 99 101 1
32 101B95068 40 1 99 101 1
33 538B70011 51 1 10 538 1
34 689C85036 57 1 1 689 1
35 689C95450 57 1 1 689 1
36 556B85050 62 1 12 556 1
37 636B80005 62 1 23 636 1
38 636B92002 62 1 23 636 1
39 630B30005 70 1 2 630 1
40 642B80021 78 1 4 642 1
41 101B79173 86 1 99 101 1
42 523B81007 106 0 1 523 1
43 620B88003 106 0 2 620 1
44 642B40002 106 1 4 642 1
45 642B40001 106 1 4 642 1
46 581B81002 106 0 5 581 1
47 581B81001 106 0 5 581 1
48 573B95000 106 0 8 573 1
49 589B80015 106 0 15 589 1
50 589B80016 106 0 15 589 1
51 657B50013 106 0 15 657 1
52 657B43004 106 0 15 657 1
53 459B85085 106 0 21 459 1
54 459Y81171 106 0 21 459 1
55 101B75006 106 0 99 101 1
56 101SC8023 106 0 99 101 1
57 101B85122 106 0 99 101 1
58 101B55116 106 0 99 101 1
59 101B79086 106 0 99 101 1
60 101B95066 106 0 99 101 1
61 730B97005 106 0 99 730 1
62 741B85045 106 0 99 741 1
63 777B96001 106 0 99 777 1
64 556B85077 1 1 12 556 2
65 636B92003 1 1 23 636 2
66 101B94137 1 1 99 101 2
67 700C64500 5 1 99 791 2
68 463Y91171 6 1 20 463 2
69 618C84319 6 1 23 618 2
70 776C93046 6 1 99 776 2
71 556B95042 7 1 12 556 2
72 556B95043 7 1 12 556 2
73 556B97000 7 1 12 556 2
74 549B80069 7 1 17 549 2
75 573B95000 22 1 8 573 2
76 580B90024 22 1 16 580 2
77 523B81007 28 1 1 523 2
78 520B60012 32 1 16 520 2
79 520B70011 32 1 16 520 2
80 586B70008 33 1 16 586 2
81 586B80006 33 1 16 586 2
82 586B80011 33 1 16 586 2
83 586B80015 33 1 16 586 2
84 657B43004 34 1 15 657 2
85 636B99009 35 1 23 636 2
86 691B68018 36 1 22 691 2
87 657B50013 41 1 15 657 2
88 741B95031 42 1 99 741 2
89 620B88003 46 0 2 620 2
90 620B90008 46 0 2 620 2
91 581B81001 46 0 5 581 2
92 581B81002 46 0 5 581 2
93 552B99002 46 0 10 552 2
94 459B85085 46 0 21 459 2
95 459B95055 46 0 21 459 2
96 101B75006 46 0 99 101 2
97 101B55060 46 0 99 101 2
98 101B79086 46 0 99 101 2
99 101B79058 46 0 99 101 2
100 101B85122 46 0 99 101 2
101 101B89115 46 0 99 101 2
102 101B85047 46 0 99 101 2
103 101B94123 46 0 99 101 2
104 101B95091 46 0 99 101 2
105 101B95038 46 0 99 101 2
106 101D98001 46 0 99 101 2
107 730B97005 46 0 99 730 2
108 741B85045 46 0 99 741 2
Here is my code for the Shiny App:
library(shiny)
library(ggplot2)
library(survival)
library(survminer)
library(dplyr)
attach(tdata)
studychoices=unique(tdata$Study)
groupchoices=unique(tdata$Group)
# Define UI
ui <- fluidPage(
titlePanel("Survival Data"),
selectInput(inputId = "studyselector",label="Select a Study:", choices=studychoices),
selectInput(inputId = "groupselector",label="Select a Group:", choices=groupchoices),
plotOutput("p1")
)
# Define server logic
server <- function(input, output) {
filter=reactive({
filteredData=tdata[tdata$Study==input$studyselector,]
return(filteredData)
})
output$p1=renderPlot({
fit=survfit(Surv(Time,Censored)~input$groupselector,data=filter())
ggsurvplot(fit,data=filter(),pval=TRUE,xlim=c(0,max(Time)+1),
title=paste("Study","INSERT HERE STUDY #", "Survival Plot for Group","INSERT HERE GROUP #"),
xlab="Time (Days)",
ggtheme=theme(plot.title=element_text(hjust=0.5)))
})
}
# Run the application
shinyApp(ui = ui, server = server)
I have the following two questions:
1.) When I run the App, I get an error in an external window that reads, "Error: variable lengths differ (found for'input$groupselector'). There are no NAs in this data and I specified the data to be used is the filter() dataset based on the Study selection so I'm not sure why this error is popping up.
2.) How would I be able to dynamically change the Study # and the Group # in the title? I understand how to do that with a normal R function, but I'm a little lost with the Shiny set up.
Any help would be appreciated! Thank you!
Solution
Edited solution
This should now work - have edited the Group column to be a binary in/out when passed to your reactive dataframe, which should colour the lines appropriately:
library(tidyverse)
library(survival)
library(survminer)
library(shiny)
ui <- fluidPage(
titlePanel("Survival Data"),
selectInput(inputId = "studyselector",label="Select a Study:", choices=studychoices),
selectInput(inputId = "groupselector",label="Select a Group:", choices=groupchoices),
plotOutput("p1")
)
# Define server logic
server <- function(input, output) {
filter=reactive({
filteredData=data[data$Study==input$studyselector,]
filteredData['Group'] = ifelse(filteredData$Group==input$groupselector,
input$groupselector,
"Others")
return(filteredData)
})
output$p1=renderPlot({
fit=survfit(Surv(Time,Censored)~Group,data=filter()) # `Group` as variable to stratify by?
ggsurvplot(fit,data=filter(),pval=TRUE,xlim=c(0,max(filter()$Time)+1),
title=paste("Study",
input$studyselector, # paste these bits straight in
"Survival Plot for Group",
input$groupselector), # here too
xlab="Time (Days)",
ggtheme=theme(plot.title=element_text(hjust=0.5)))
})
}
# Run the application
shinyApp(ui = ui, server = server)
Do let me know in comments if there are any mistakes or further ideas/questions!
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