bin/build_survival_curves.R

File

build_survival_curves.R

Usage

bin/build_survival_curves.R [options]

Fit the Kaplan-Meier survival curves and a Cox proportional hazards model using the R ‘survival’ package.

Options
--input_fp=INPUT_FP

Path to the xlsx input file

--model=MODEL

R formula for the survival::survfit() function

-o OUTPUT, --output_dir=OUTPUT_DIR

Path to the output directory. Default: data

-f FIG_DIR, --fig_dir=FIG_DIR

Path to the output directory for figure. Default: same as –output_dir

--prism=PRISM

Also generate a Graphpad Prism-compatible TXT table? (TRUE or FALSE) Default: TRUE

-c COLORS, --colors=COLORS

You can specify a comma-delimited set of colors. ex: “#FBB040,#F15A29,#00AEEF,#272BFF”

--legendpos=LEGENDPOS

Figure legend position. (top, right, bottom or left) Default: right

--figdata=FIGDATA

Generate a RDS file for the figure? (TRUE or FALSE) Default: TRUE

--txt=TXT

Name of the output TXT table. Default: survival_data.txt

--pdf=PDF

Name of the output PDF figure. Default: survival_data.pdf

--coxph=COXPH

Name of the output file for the Cox proportional hazards model. Default: coxph.txt

--km=KM

Name of the output file for the Kaplan-Meier survival model. Default: km.txt

-h, --help

Show this help message and exit

Outputs

  • A tidy data table. Default to data/survival_data.txt.

  • If --prism is TRUE, a data table in a Graphpad Prism-compatible format. Default to data/survival_data.txt-PRISM.txt.

    • The results of the Cox regression analysis. Default to data/coxph.txt.

    • A data table of variable for the Kaplan-Meier model. Default to data/km.txt.

    • The figures, including survival curves. Default to data/survival_data.pdf.

    • IF --figdata is TRUE, the figures data in RDS format. Default to data/survival_data.rds.

    The RDS file contains a list with the following elements:

    • km: Kaplan-Meier survival curves

    • km.straight: Straight-line version of the Kaplan-Meier survival curves

    • n.risk: Number of individuals at risk over time

    • perc.risk: Number of individuals at risk over time as a percentage of initial number

    • median: Median survival time with 0.95 confidence interval

    • mean: Mean survival time with Standard Error

    • mrad: Maximum reported age at death

    • quartiles: Survival time quartiles and Maximum reported age at death

    • coxph: Cox proportional hazard ratio for each covariate