km.plot: Kaplan-Meier Survival Plot
In emwozniak/kmrskplot: Survival Plots

Description Usage Arguments Value Author(s) Examples

This function generates Kaplan-Meier survival curves.

km_plot(fit, type, xlim_major, xlim_minor, ylim_major, ylim_minor, grid, col_grid_major, col_grid_minor, lwd_grid_major, lwd_grid_minor, conf_int, mark_time, col, lty, lwd, plot_title, plot_title_size, plot_subtitle, plot_subtitle_size, x_axis_label, y_axis_label, axis_label_size, extra_left_margin, font_family, print_risk_table, print_group_lines, print_group_names, risk_table_title, group_names, group_order, legend, legend_x_loc, legend_y_loc)

`fit`	Fitted model object from `survfit`. Required.
`type`	Kaplan-Meier plot ("km") or complement ("1-km"). Optional; defaults to "km".
`xlim_major`	Vector of x-axis locations for labels and major gridlines. Optional.
`xlim_minor`	Vector of x-axis locations for minor gridlines. Optional.
`ylim_major`	Vector of y-axis locations for labels and major gridlines. Optional.
`ylim_minor`	Vector of y-axis locations for minor gridlines. Optional.
`grid`	Plot gridlines? Optional logical; defaults to TRUE.
`col_grid_major`	Color of major gridlines. Optional.
`col_grid_minor`	Color of minor gridlines. Optional.
`lwd_grid_major`	Line width of major gridlines. Optional.
`lwd_grid_minor`	Line width of minor gridlines. Optional.
`conf_int`	Plot confidence intervals? Optional logical; defaults to FALSE.
`mark_time`	Plot censoring tick marks? Optional logical; defaults to FALSE.
`col`	Vector of colors for plotted curves. Optional; defaults to ordered rainbow colors.
`lty`	Vector of line types for plotted curves. Optional; defaults to all solid.
`lwd`	Vector of line widths for plotted curves. Optional; defaults to 1.
`plot_title`	Main plot title. Optional.
`plot_title_size`	Text size for plot title. Optional.
`plot_subtitle`	Subtitle for plot. Optional.
`plot_subtitle_size`	Text size for plot subtitle. Optional.
`x_axis_label`	Label for the x-axis. Optional; defaults to "Time".
`y_axis_label`	Label for the y-axis. Optional; defaults to "Probability".
`axis_label_size`	Text size for axis labels. Optional.
`extra_left_margin`	Increase numeric value for added left margin padding to accomodate long labels. Optional.
`font_family`	Choice of "sans", "serif", "mono", or a specified font set up to work on the user's system. Optional; defaults to "serif".
`print_risk_table`	Print risk table beneath plot? Optional logical; defaults to TRUE.
`print_group_lines`	Print legend lines next to risk table? Optional logical; defaults to TRUE.
`print_group_names`	Print group/strata names next to risk table? Optional logical; defaults to TRUE.
`risk_table_title`	Header for risk table. Optional; defaults to "Total at risk".
`group_names`	Vector of group names to print in risk table. Optional.
`group_order`	Numeric vector giving order of groups to be printed in risk table. Optional.
`legend`	Logical indicator for printing a legend on the plot. Optional; defaults to FALSE since the information is found by default in the risk table.
`legend_x_loc`	X-axis coordinate or position for the legend location. Optional; defaults to "bottomleft".
`legend_y_loc`	Y-axis coordinate for the legend location. Optional; defaults to NULL.

Returns a Kaplan-Meier plot with the requested attributes.

Erica Wozniak

library(survival)

# Set up data as a survival object
# KM plot for time to death
# Censor those who receive a transplant or are indicated by the dataset as censored
pbc_km <- na.omit(pbc[, c("time", "status", "trt")])
pbc_km$status[pbc_km$status == 1] <- 0
pbc_km$status[pbc_km$status == 2] <- 1
pbc_km$SurvObj <- with(pbc_km, 
                       Surv(time  = time, 
                            event = status)
                            )
fit <- survfit(SurvObj ~ trt, 
               data = pbc_km, 
               conf.type = "log-log")
               
# Usage note: if gridlines are extending outside the plot border, run
# "dev.off()" and then run the plotting function again.
               
# Default options only
km_plot(fit = fit)

# Customized pretty plot with some options
km_plot(fit  = fit,
        type = "km",
        col  = c("orange3", "olivedrab"),
        # Add an extra major gridline and risk table column at time 4500
        xlim_major    = c(0, 1000, 2000, 3000, 4000, 4500, 5000),
        plot_title    = "Primary biliary cirrhosis survival",
        plot_subtitle = "By randomized treatment status",
        y_axis_label  = "Survival",
        x_axis_label  = "Time since registration (days)",
        group_names   = c("D-penacillamine", "Placebo"),
        risk_table_title = bquote(italic("Patients at risk:")))

# Customized retro plot with lots of options
km_plot(fit  = fit,
        font_family = "mono",
        type = "1-km",
        col  = c("black", "black"),
        lty  = c(1, 2),
        lwd  = c(2, 2),
        xlim_major = c(0, 500, 1000, 2000, 3000, 3375, 4000, 4500, 5000),
        col_grid_major = "gray80",
        col_grid_minor = "gray92",
        plot_title = bquote(bold("Death following transplant registration")),
        plot_subtitle = "Mayo Clinic 1974-1984",
        plot_title_size = 1,
        y_axis_label = bquote(bold("Cumulative incidence")),
        x_axis_label = bquote(bold("Days")),
        group_names  = c("D-penacillamine", "Placebo"),
        group_order  = c(2, 1),
        risk_table_title  = bquote(bold(underline("RISK TABLE"))),
        extra_left_margin = 5)