Problem with lapply, object not found when trying to use dataframe from list

Question

I have a list of dataframes that I want to filter and get a list of their plots. I have provided the 3 df of my lists and the 10 first rows of every df

library(dplyr)
library(survival)
library(survminer)

df_list<-list(STAT5A = structure(list(Months = c(114.3333333, 257.7666667, 
                                                 242.5666667, 240.4333333, 117.5333333, 153.9666667, 131.0666667, 
                                                 67.46666667, 2.5, 271.2666667), Evento = c(0L, 0L, 0L, 0L, 0L, 
                                                                                            0L, 0L, 0L, 0L, 0L), Gen.Alt = c("Low.Amp650", "Low.Amp650", 
                                                                                                                             "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650", 
                                                                                                                             "Low.Amp650", "Low.Amp650", "Low.Amp650")), row.names = c("MB-0508", 
                                                                                                                                                                                       "MB-3122", "MB-5190", "MB-5444", "MB-7109", "MB-0062", "MB-0218", 
                                                                                                                                                                                       "MB-0500", "MB-0522", "MB-2801"), class = "data.frame"), THBD = structure(list(
                                                                                                                                                                                         Months = c(214.7, 242.5666667, 243.1666667, 117.5333333, 
                                                                                                                                                                                                    153.9666667, 114.6, 261.2, 163.5333333, 200.1333333, 234.4
                                                                                                                                                                                         ), Evento = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Gen.Alt = c("Low.Amp650", 
                                                                                                                                                                                                                                                            "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650", 
                                                                                                                                                                                                                                                            "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650")), row.names = c("MB-3600", 
                                                                                                                                                                                                                                                                                                                                    "MB-5190", "MB-5366", "MB-7109", "MB-0062", "MB-0605", "MB-2984", 
                                                                                                                                                                                                                                                                                                                                    "MB-5327", "MB-5541", "MB-5566"), class = "data.frame"), PER2 = structure(list(
                                                                                                                                                                                                                                                                                                                                      Months = c(239.3, 262.6333333, 282.3666667, 78.76666667, 
                                                                                                                                                                                                                                                                                                                                                 153.9666667, 131.0666667, 67.46666667, 76.7, 97.26666667, 
                                                                                                                                                                                                                                                                                                                                                 243.7666667), Evento = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
                                                                                                                                                                                                                                                                                                                                                                          0L, 0L), Gen.Alt = c("Low.Amp650", "Low.Amp650", "Low.Amp650", 
                                                                                                                                                                                                                                                                                                                                                                                               "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650", "Low.Amp650", 
                                                                                                                                                                                                                                                                                                                                                                                               "Low.Amp650", "Low.Amp650")), row.names = c("MB-3500", "MB-3014", 
                                                                                                                                                                                                                                                                                                                                                                                                                                           "MB-6062", "MB-0174", "MB-0062", "MB-0218", "MB-0500", "MB-0610", 
                                                                                                                                                                                                                                                                                                                                                                                                                                           "MB-0658", "MB-3395"), class = "data.frame"))
loop<-c(1:length(df_list))
Alteraciones<-c("Low.Amp650","Low","High")
survival<-function(i){
  Gen.Surv<-df_list[[i]]
  s<-filter(Gen.Surv,Gen.Alt%in%Alteraciones[c(1:2)])
  a.km <- survfit(Surv(Months, Evento) ~ Gen.Alt, data = s, type = "kaplan-meier")
  plot_i<-ggsurvplot(a.km, conf.int=FALSE)
}
graphs<-lapply(loop,FUN=survival)
arrange_ggsurvplots(graphs,nrow=2,ncol=2)

But I get the following error

Error in eval(fit$call$data) : object 's' not found
Called from: eval(fit$call$data)
Error during wrapup: unimplemented type (29) in 'eval'

Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error during wrapup: INTEGER() can only be applied to a 'integer', not a 'unknown type #29'
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

For some reason, this chunk of code is not working

     Gen.Surv<-df_list[[i]]
  s<-filter(Gen.Surv,Gen.Alt%in%Alteraciones[c(1:2)])

But if I run it this way it works well (1 instead of i)

x<-df_list[[1]]
y<-filter(x,Gen.Alt%in%Alteraciones[c(1:2)])
a.km <- survfit(Surv(Months, Evento) ~ Gen.Alt, data = y, type = "kaplan-meier")
plot_1<-ggsurvplot(a.km, conf.int=FALSE)
graphs<-list(plot_1,plot_2,plot_3)
arrange_ggsurvplots(graphs,nrow=2,ncol=2)

I could make it work for every plot, one by one but what if I had more DF? I would like to get my 3 different plots like this I would appreciate any help.

It's easier to help you if you include a simple [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input and desired output that can be used to test and verify possible solutions. Can you define `DF1`, `DF2`, and `DF3` so we can run and test the code ourselves? — MrFlick, Jul 06 '20 at 01:43
Thanks, I have edited my question and I have added a subset of my data to run and the plot I should get. I hope this time is better, it is my first post. — Eric Lopez Huerta, Jul 07 '20 at 17:01

score 0 · Accepted Answer · answered Jul 07 '20 at 20:48

From this surviminor github issue, the problem is that you need to pass the data= info to ggsurvplot. So just change your function to

survival<-function(i){
  Gen.Surv <- df_list[[i]]
  s <- filter(Gen.Surv,Gen.Alt%in%Alteraciones[c(1:2)])
  a.km <- survfit(Surv(Months, Evento) ~ Gen.Alt, data = s, type = "kaplan-meier")
  ggsurvplot(a.km, conf.int=FALSE, data=s)
}

Problem with lapply, object not found when trying to use dataframe from list

1 Answers1