kmTCGA: Plot Kaplan-Meier Estimates of Survival Curves for Survival...

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

Plot Kaplan-Meier Estimates of Survival Curves for Survival Data

Description

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

Usage

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,
  ggtheme = theme_RTCGA(),
  ...
)

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?
ggtheme	a ggtheme to be used (set to NULL, if using ggthemr package)
...	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.

Author(s)

Marcin Kosinski, [e-mail]

See Also

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

Other RTCGA: RTCGA-package, boxplotTCGA(), checkTCGA(), convertTCGA(), 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)

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.