TCGAanalyze_survival {TCGAbiolinks} | R Documentation |
Creates a survival plot from TCGA patient clinical data using survival library. It uses the fields days_to_death and vital, plus a columns for groups.
TCGAanalyze_survival( data, clusterCol = NULL, legend = "Legend", labels = NULL, risk.table = TRUE, xlim = NULL, main = "Kaplan-Meier Overall Survival Curves", ylab = "Probability of survival", xlab = "Time since diagnosis (days)", filename = "survival.pdf", color = NULL, height = 8, width = 12, dpi = 300, pvalue = TRUE, conf.int = TRUE, ... )
data |
TCGA Clinical patient with the information days_to_death |
clusterCol |
Column with groups to plot. This is a mandatory field, the caption will be based in this column |
legend |
Legend title of the figure |
labels |
labels of the plot |
risk.table |
show or not the risk table |
xlim |
x axis limits e.g. xlim = c(0, 1000). Present narrower X axis, but not affect survival estimates. |
main |
main title of the plot |
ylab |
y axis text of the plot |
xlab |
x axis text of the plot |
filename |
The name of the pdf file. |
color |
Define the colors/Pallete for lines. |
height |
Image height |
width |
Image width |
dpi |
Figure quality |
pvalue |
show p-value of log-rank test |
conf.int |
show confidence intervals for point estimates of survival curves. |
... |
Further arguments passed to ggsurvplot. |
Survival plot
# clin <- GDCquery_clinic("TCGA-BRCA","clinical") clin <- data.frame( vital_status = c("alive","alive","alive","dead","alive", "alive","dead","alive","dead","alive"), days_to_death = c(NA,NA,NA,172,NA,NA,3472,NA,786,NA), days_to_last_follow_up = c(3011,965,718,NA,1914,423,NA,5,656,1417), gender = c(rep("male",5),rep("female",5)) ) TCGAanalyze_survival(clin, clusterCol="gender") TCGAanalyze_survival(clin, clusterCol="gender", xlim = 1000) TCGAanalyze_survival(clin, clusterCol="gender", risk.table = FALSE, conf.int = FALSE, color = c("pink","blue")) TCGAanalyze_survival(clin, clusterCol="gender", risk.table = FALSE, xlim = c(100,1000), conf.int = FALSE, color = c("Dark2"))