ggkmcif {reportRmd}

Plot KM and CIF curves with ggplot

Description

This function will plot a KM or CIF curve with option to add the number at risk. You can specify if you want confidence bands, the hazard ratio, and pvalues, as well as the units of time used.

Usage

ggkmcif(
  response,
  cov = NULL,
  data,
  type = NULL,
  pval = TRUE,
  HR = FALSE,
  HR_pval = FALSE,
  conf.curves = FALSE,
  conf.type = "log",
  table = TRUE,
  times = NULL,
  xlab = "Time",
  ylab = NULL,
  main = NULL,
  stratalabs = NULL,
  strataname = nicename(cov),
  stratalabs.table = NULL,
  strataname.table = strataname,
  median.text = FALSE,
  median.lines = FALSE,
  median.CI = FALSE,
  set.time.text = NULL,
  set.time.line = FALSE,
  set.time = 5,
  set.time.CI = FALSE,
  censor.marks = TRUE,
  censor.size = 3,
  censor.stroke = 1.5,
  fsize = 10,
  nsize = 3,
  lsize = 1,
  psize = 3.5,
  median.size = 3,
  median.pos = NULL,
  median.lsize = 1,
  set.size = 3,
  set.pos = NULL,
  set.lsize = 1,
  ylim = c(0, 1),
  col = NULL,
  linetype = NULL,
  xlim = NULL,
  legend.pos = NULL,
  pval.pos = NULL,
  plot.event = 1,
  event = c("col", "linetype"),
  flip.CIF = FALSE,
  cut = NULL,
  eventlabs = NULL,
  event.name = NULL,
  Numbers_at_risk_text = "Numbers at risk",
  HR.digits = 2,
  HR.pval.digits = 3,
  pval.digits = 3,
  median.digits = 3,
  set.time.digits = 3,
  returns = FALSE,
  print.n.missing = TRUE
)

Arguments

response

character vector with names of columns to use for response

cov

String specifying the column name of stratification variable

data

dataframe containing your data

type

string indicating he type of univariate model to fit. The function will try and guess what type you want based on your response. If you want to override this you can manually specify the type. Options include "KM", and ,"CIF"

pval

boolean to specify if you want p-values in the plot (Log Rank test for KM and Gray's test for CIF)

HR

boolean to specify if you want hazard ratios included in the plot

HR_pval

boolean to specify if you want HR p-values in the plot

conf.curves

boolean to specify if you want confidence interval bands

conf.type

One of "none"(the default), "plain", "log" , "log-log" or "logit". Only enough of the string to uniquely identify it is necessary. The first option causes confidence intervals not to be generated. The second causes the standard intervals curve +- k *se(curve), where k is determined from conf.int. The log option calculates intervals based on the cumulative hazard or log(survival). The log-log option bases the intervals on the log hazard or log(-log(survival)), and the logit option on log(survival/(1-survival)).

table

Logical value. If TRUE, includes the number at risk table

times

Numeric vector of times for the x-axis

xlab

String corresponding to xlabel. By default is "Time"

ylab

String corresponding to ylabel. When NULL uses "Survival probability" for KM cuves, and "Probability of an event" for CIF

main

String corresponding to main title. When NULL uses Kaplan-Meier Plot s, and "Cumulative Incidence Plot for CIF"

stratalabs

string corresponding to the labels of the covariate, when NULL will use the levels of the covariate

strataname

String of the covariate name default is nicename(cov)

stratalabs.table

String corresponding to the levels of the covariate for the number at risk table, when NULL will use the levels of the covariate. Can use a string of "-" when the labels are long

strataname.table

String of the covariate name for the number at risk table default is nicename(cov

median.text

boolean to specify if you want the median values added to the legend (or as added text if there are no covariates), for KM only

median.lines

boolean to specify if you want the median values added as lines to the plot, for KM only

median.CI

boolean to specify if you want the 95\ with the median text (Only for KM)

set.time.text

string for the text to add survival at a specified time (eg. year OS)

set.time.line

boolean to specify if you want the survival added as lines to the plot at a specified point

set.time

Numeric values of the specific time of interest, default is 5 (Multiple values can be entered)

set.time.CI

boolean to specify if you want the 95\ interval with the set time text

censor.marks

logical value. If TRUE, includes censor marks (only for KM curves)

censor.size

size of censor marks, default is 3

censor.stroke

stroke of censor marks, default is 1.5

fsize

font size

nsize

font size for numbers in the numbers at risk table

lsize

line size

psize

size of the pvalue

median.size

size of the median text (Only when there are no covariates)

median.pos

vector of length 2 corresponding to the median position (Only when there are no covariates)

median.lsize

line size of the median lines

set.size

size of the survival at a set time text (Only when there are no covariates)

set.pos

vector of length 2 corresponding to the survival at a set point position (Only when there are no covariates)

set.lsize

line size of the survival at set points

ylim

vector of length 2 corresponding to limits of y-axis. Default to NULL

col

vector of colours

linetype

vector of line types

xlim

vector of length 2 corresponding to limits of x-axis. Default to NULL

legend.pos

Can be either a string corresponding to the legend position ("left","top", "right", "bottom", "none") or a vector of length 2 corresponding to the legend position (uses normalized units (ie the c(0.5,0.5) is the middle of the plot))

pval.pos

vector of length 2 corresponding to the p-value position

plot.event

Which event(s) to plot (1,2, or c(1,2))

event

String specifying if the event should be mapped to the colour, or linetype when plotting both events to colour = "col", line type

flip.CIF

boolean to flip the CIF curve to start at 1

cut

numeric value indicating where to divide a continuous covariate (default is the median)

eventlabs

String corresponding to the event type names

event.name

String corresponding to the label of the event types

Numbers_at_risk_text

String for the label of the number at risk

HR.digits

Number of digits printed of the hazard ratio

HR.pval.digits

Number of digits printed of the hazard ratio pvalue

pval.digits

Number of digits printed of the Gray's/log rank pvalue

median.digits

Number of digits printed of the median pvalue

set.time.digits

Number of digits printed of the probability at a specified time

returns

Logical value returns a list with all ggplot objects in a list

print.n.missing

Logical, should the number of missing be shown !Needs to be checked

Details

Note that for proper pdf output of special characters the following code needs to be included in the first chunk of the rmd knitr::opts_chunk$set(dev="cairo_pdf")

Value

Nothing is returned unless returns = TRUE is used. With returns = TRUE, if table=TRUE (the default) a table style graphic with survival plot and number at risk table is returned. Otherwise a plot with the survival curves is returned.

Examples

data("pembrolizumab")
# Simple plot without confidence intervals
ggkmcif(response = c('os_time','os_status'),
cov='cohort',
data=pembrolizumab)

# Plot with median survival time
ggkmcif(response = c('os_time','os_status'),
cov='sex',
data=pembrolizumab,
median.text = TRUE,median.lines=TRUE,conf.curves=TRUE)

# Plot with specified survival times and log-log CI
ggkmcif(response = c('os_time','os_status'),
cov='sex',
data=pembrolizumab,
median.text = FALSE,set.time.text = 'mo OS',
set.time = c(12,24),conf.type = 'log-log',conf.curves=TRUE)

# KM plot with 95% CI and censor marks
ggkmcif(c('os_time','os_status'),'sex',data = pembrolizumab, type = 'KM',
HR=TRUE, HR_pval = TRUE, conf.curves = TRUE,conf.type='log-log',
set.time.CI = TRUE, censor.marks=TRUE)