KM plot — wrapper_KM_plot_core • BiomarkerWrappers

KM plot

Usage

wrapper_KM_plot_core(
  data,
  tte_var,
  censor_var,
  covariate_var,
  colors = NULL,
  linetypes = 1,
  variable_names = NULL,
  title = TRUE,
  subtitle = TRUE,
  xlab = TRUE,
  legend_colors_title = TRUE,
  legend_position = c(0.03, 0.03),
  legend_justification = c(0, 0),
  break_time_by = NULL,
  max_tte = NULL,
  risk_table = TRUE,
  conf_int = FALSE,
  surv_median_line = "none",
  ggtheme = ggplot2::theme_get(),
  line_size = 1,
  title_size = NULL,
  label_size = NULL,
  rel_heights = c(5, 1),
  background_grid_major = "none",
  level_mapping = NULL,
  risk_table_labels = TRUE,
  print_hr = FALSE,
  print_mst = FALSE,
  print_pvalues = FALSE,
  print_options = NULL,
  cox_covariate_var = NULL,
  cox_strat_var = NULL
)

wrapper_KM_plot_core_strat(
  data,
  tte_var,
  censor_var,
  covariate_var,
  strat1_var = NULL,
  strat2_var = NULL,
  colors = NULL,
  linetypes = 1,
  variable_names = NULL,
  title = TRUE,
  xlab = TRUE,
  strat1_label_both = TRUE,
  strat2_label_both = TRUE,
  legend_colors_title = TRUE,
  legend_position = c(0.03, 0.03),
  legend_justification = c(0, 0),
  break_time_by = NULL,
  max_tte = NULL,
  risk_table = TRUE,
  conf_int = FALSE,
  surv_median_line = "none",
  ggtheme = ggplot2::theme_get(),
  line_size = 1,
  title_size = NULL,
  label_size = NULL,
  rel_heights = c(5, 1),
  background_grid_major = "none",
  level_mapping = NULL,
  risk_table_labels = TRUE,
  print_hr = FALSE,
  print_mst = FALSE,
  print_pvalues = FALSE,
  print_options = NULL,
  cox_covariate_var = NULL,
  cox_strat_var = NULL,
  strat_scales = "fixed",
  strat1_nrow = 1,
  strat1_ncol = NULL,
  strat2_nrow = NULL,
  strat2_ncol = 1
)

Arguments

data: Data frame.
tte_var: Name of the variable containing time-to-event data.
censor_var: Name of the variable containing censoring information. Censor variable must be numeric and encode 1 for event and 0 for censor.
covariate_var: Name of variable that defines the subgroups where the survival is calculated. This variable must be a factor.
level_mapping: Named vector with level mapping. The names correspond to the original levels of covariate_var.
risk_table_labels: Possible values: "levels", "shape"
print_options: Named vector. The default is c(npcx = 1, npcy = 0.05, hjust = 1, vjust = 0, size = 4) for text in the bottom right corner. For text in the top right corner use c(npcx = 1, npcy = 1, hjust = 1, vjust = 1, size = 4)
strat1_var: Name of the firts stratification variable.
strat2_var: Name of the second stratification variable.

Examples


data(bdata)

data <- bdata

tte_var <- "PFS"
censor_var <- "PFS_Event"
covariate_var <- "Treatment_Arm"


wrapper_KM_plot_core(data = data, tte_var = tte_var, censor_var = censor_var, covariate_var = covariate_var)



data(bdata)

data <- bdata
data$GeneA_cat2 <- wrapper_cut_2groups(data$GeneA)

tte_var <- "PFS"
censor_var <- "PFS_Event"
covariate_var <- "GeneA_cat2"

strat1_var = "Treatment_Arm"
strat2_var = "Cell_Of_Origin"


wrapper_KM_plot_core_strat(data = data, tte_var = tte_var, censor_var = censor_var, covariate_var = covariate_var, strat1_var = strat1_var, strat2_var = strat2_var)