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Question: error/warning message while doing kmTCGA survival plot
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gravatar for colonppg
9 weeks ago by
colonppg10
United States
colonppg10 wrote:

anyone encountered the same message while using kmTCGA?

Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale.
Warning message:
In .get_data(fit, data = data) :
  The `data` argument is not provided. Data will be extracted from model fit.
 

Many thanks! By the way, Is there play to update the RTCGA package to the latest TCGA data?

Thanks

ADD COMMENTlink modified 5 weeks ago by jpgsabino0 • written 9 weeks ago by colonppg10
0
gravatar for jpgsabino
5 weeks ago by
jpgsabino0
jpgsabino0 wrote:

Hello,

I am using ggsurvplot (package survminer) and I had the same problem:

Warning message:
In .get_data(fit, data = data) :
  The `data` argument is not provided. Data will be extracted from model fit.

kmTCGA uses ggsurvplot to plot the nice Kaplan Meier. Probably the issue lies there.

 

  Dataset$TimeToEvent <- with(Dataset, Surv(Time_to_event, Event == 1))
  fit <- survfit(TimeToEvent ~ 1, data=Dataset, conf.type = "log")  
  ggsurvplot(
   fit,    # survfit object with calculated statistics.
   data=Dataset,            # dataset
   risk.table = TRUE,       # show risk table.
   ncensor.plot=TRUE,
   risk.table.y.text=FALSE,
   legend.title = "",
   conf.int = TRUE       # show confidence intervals for 
                            # point estimaes of survival curves.
    )

 

If you don't specify the data=Dataset you will get the message.

Reference: https://github.com/kassambara/survminer/pull/135/files

 

Grts

 

 

 

ADD COMMENTlink written 5 weeks ago by jpgsabino0
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