Plot Kaplan-Meier Estimates of Survival Curves for Survival Data

Plots Kaplan-Meier estimates of survival curves for survival data.

kmTCGA(x, times = "times", status = "patient.vital_status",
  explanatory.names = "1", main = "Survival Curves", risk.table = TRUE,
  risk.table.y.text = FALSE, conf.int = TRUE, return.survfit = FALSE,
  pval = FALSE, ...)

Arguments

x
A data.frame containing survival information. See survivalTCGA.
times
The name of time variable.
status
The name of status variable.
explanatory.names
Names of explanatory variables to use in survival curves plot.
main
Title of the plot.
risk.table
Whether to show risk tables.
risk.table.y.text
Whether to show long strata names in legend of the risk table.
conf.int
Whether to show confidence intervals.
return.survfit
Should return survfit object additionaly to survival plot?
pval
Whether to add p-value of the log-rank test to the plot?
...
Further arguments passed to ggsurvplot.

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

See also

RTCGA website http://rtcga.github.io/RTCGA/articles/Visualizations.html.

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, convertTCGA, createTCGA, datasetsTCGA, downloadTCGA, expressionsTCGA, heatmapTCGA, infoTCGA, installTCGA, mutationsTCGA, pcaTCGA, readTCGA, survivalTCGA, theme_RTCGA

Examples


## Extracting Survival Data
library(RTCGA.clinical)
survivalTCGA(BRCA.clinical, OV.clinical, extract.cols = "admin.disease_code") -> BRCAOV.survInfo

## Kaplan-Meier Survival Curves
kmTCGA(BRCAOV.survInfo, explanatory.names = "admin.disease_code",  pval = TRUE)

kmTCGA(BRCAOV.survInfo, explanatory.names = "admin.disease_code", main = "",
       xlim = c(0,4000))

# first munge data, then extract survival info
library(dplyr)
BRCA.clinical %>%
    filter(patient.drugs.drug.therapy_types.therapy_type %in%
               c("chemotherapy", "hormone therapy")) %>%
    rename(therapy = patient.drugs.drug.therapy_types.therapy_type) %>%
    survivalTCGA(extract.cols = c("therapy"))  -> BRCA.survInfo.chemo

# first extract survival info, then munge data                  
    survivalTCGA(BRCA.clinical,
                 extract.cols = c("patient.drugs.drug.therapy_types.therapy_type"))  %>%
    filter(patient.drugs.drug.therapy_types.therapy_type %in%
               c("chemotherapy", "hormone therapy")) %>%
    rename(therapy = patient.drugs.drug.therapy_types.therapy_type) -> BRCA.survInfo.chemo


kmTCGA(BRCA.survInfo.chemo, explanatory.names = "therapy",
       xlim = c(0, 3000), conf.int = FALSE)