Component: KaplanMeier

KaplanMeier

Produces a Kaplan-Meier plot representing survival estimates based on the given data.

Version	2.2
Bundle	tools
Categories	Survival Latex
Authors	Marko Laakso (Marko.Laakso@Helsinki.FI), Riku Louhimo (Riku.Louhimo@Helsinki.FI), Kristian Ovaska (kristian.ovaska@helsinki.fi), Ali Faisal (ali.faisal@aalto.fi)
Issue tracker	View/Report issues
Requires	survival (R-package)
Source files	component.xml KaplanMeier.r
Usage	Example with default values KaplanMeier( survival = CSV, //annotation = AnnotationTable, PLimit = 1.00, annotCol = "*", confInt = 0.95, contiCols = "", eventSymbol = "1", excludeCol = "", groupCol = "", minCount = 0, minGroups = 0, modelVarCols = "", printTable = false, statusCol = <string>, strataCols = "", timeCol = <string>, timeOutLimit = -1, title = "Kaplan-Meier survival estimates", xLabel = "survival time" )

Version

2.2

Bundle

tools

Categories

Survival Latex

Authors

Marko Laakso (Marko.Laakso@Helsinki.FI), Riku Louhimo (Riku.Louhimo@Helsinki.FI), Kristian Ovaska (kristian.ovaska@helsinki.fi), Ali Faisal (ali.faisal@aalto.fi)

Issue tracker

View/Report issues

Requires

survival (R-package)

Source files

component.xml KaplanMeier.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
survival	CSV	Mandatory	Survival time and event indicators, and the sample group assignments.
annotation	AnnotationTable	Optional	Additional annotations for the groupCol names. These annotations are listed as column name value pairs in figure caption.

Name

Type

Mandatory

Description

survival

CSV

Mandatory

Survival time and event indicators, and the sample group assignments.

annotation

AnnotationTable

Optional

Additional annotations for the groupCol names. These annotations are listed as column name value pairs in figure caption.

Outputs

Name	Type	Description
report	Latex	LaTeX-document for the plots and summary
statistics	CSV	Kaplan-Meier statistics for the sample groups. All plotted groups are present; in addition, groups for which the p-value is above PLimit are present in this table but they are not plotted. This table contains also file names of the document figures. If a group was not plotted, the file name is NA.
plots	Array<PDF>	An array of the Kaplan-Meier curves that are also part of the report

Name

Type

Description

report

Latex

LaTeX-document for the plots and summary

statistics

CSV

Kaplan-Meier statistics for the sample groups. All plotted groups are present; in addition, groups for which the p-value is above PLimit are present in this table but they are not plotted. This table contains also file names of the document figures. If a group was not plotted, the file name is NA.

plots

Array<PDF>

An array of the Kaplan-Meier curves that are also part of the report

Parameters

Name	Type	Default	Description
PLimit	float	1.00	Ignore results with a p-value greater than this limit
annotCol	string	"*"	A comma separated list of column names of the annotation file that will be shown in the report. An asterisk (*) may be used for all attributes except the first one that is considered as a key.
confInt	float	0.95	Coverage of the confidence intervals [0,1] or a negative number to disable them
contiCols	string	""	A comma separated list of column names that contain continuous variables (e.g., age). By default columns are assumed to contain categories.
eventSymbol	string	"1"	Value of statusCol column indicating an event. Other values are considered as censorings.
excludeCol	string	""	A comma separated list of column names that should not be used as groupCols even if an asterisk is used. This is especially useful to filter out samples identifiers and other irrelevant columns.
groupCol	string	""	A comma separated list of column names of sample group identifiers or an empty string for a single curve. An asterisk (*) may be used to plot all attributes except those defined for the other purposes or listed in excludeCol.
minCount	int	0	Individual groups with less that this many members will be left out
minGroups	int	0	No results are produced for the sets where the analysis (after the minCount pruning) consists of less than this many groups
modelVarCols	string	""	Comma separated list of column names for background variables in the Cox model. Default indicates that only the logrank test is used for p-value computation. If columns are defined here, the PLimit parameter refers to the Cox p-values.
printTable	boolean	false	Print table of number of risk individuals in seven even intervals.
statusCol	string	(no default)	Column name for the event indicator
strataCols	string	""	Comma separated list of column names for background variables that should be stratified in the Cox model.
timeCol	string	(no default)	Column name for the survival time
timeOutLimit	float	-1	Cut survival curves after this limit. A negative value can be used to maximize the length of the period.
title	string	"Kaplan-Meier survival estimates"	Figure title
xLabel	string	"survival time"	Label for the horizontal time axis

Name

Type

Default

Description

PLimit

float

1.00

Ignore results with a p-value greater than this limit

annotCol

string

"*"

A comma separated list of column names of the annotation file that will be shown in the report. An asterisk (*) may be used for all attributes except the first one that is considered as a key.

confInt

float

0.95

Coverage of the confidence intervals [0,1] or a negative number to disable them

contiCols

string

A comma separated list of column names that contain continuous variables (e.g., age). By default columns are assumed to contain categories.

eventSymbol

string

"1"

Value of statusCol column indicating an event. Other values are considered as censorings.

excludeCol

string

A comma separated list of column names that should not be used as groupCols even if an asterisk is used. This is especially useful to filter out samples identifiers and other irrelevant columns.

groupCol

string

A comma separated list of column names of sample group identifiers or an empty string for a single curve. An asterisk (*) may be used to plot all attributes except those defined for the other purposes or listed in excludeCol.

minCount

int

Individual groups with less that this many members will be left out

minGroups

int

No results are produced for the sets where the analysis (after the minCount pruning) consists of less than this many groups

modelVarCols

string

Comma separated list of column names for background variables in the Cox model. Default indicates that only the logrank test is used for p-value computation. If columns are defined here, the PLimit parameter refers to the Cox p-values.

printTable

boolean

false

Print table of number of risk individuals in seven even intervals.

statusCol

string

(no default)

Column name for the event indicator

strataCols

string

Comma separated list of column names for background variables that should be stratified in the Cox model.

timeCol

string

(no default)

Column name for the survival time

timeOutLimit

float

-1

Cut survival curves after this limit. A negative value can be used to maximize the length of the period.

title

string

"Kaplan-Meier survival estimates"

Figure title

xLabel

string

"survival time"

Label for the horizontal time axis

Test cases

Test case	Parameters▼	IN survival	IN annotation	OUT report	OUT statistics	OUT plots
case1	properties	survival	(missing)	report	statistics	plots
	timeCol = Followup, statusCol = Vitalstatus, groupCol = SNP_Add_Uncommon, minCount = 60, timeOutLimit = 30
case2_one_group	properties	survival	annotation	report	statistics	plots
	timeCol = Followup, statusCol = Vitalstatus, confInt = -1, annotCol = showMe
case3_multiple_plots	properties	survival	annotation	report	statistics	plots
	timeCol = Followup, statusCol = Vitalstatus, groupCol = , excludeCol* = ID,Dgage,Ageatlastupdate,Foll_20y,Death_20y
case4_plimit	properties	survival	(missing)	report	statistics	plots
	timeCol = Followup, statusCol = Vitalstatus, groupCol = , excludeCol* = ID, PLimit = 0.5, eventSymbol = 0, title = Kaplan-Meier test, xLabel = Ueberlebensdauer
case5_cox	properties	survival	(missing)	(missing)	statistics	plots
	excludeCol = PatientID,time,status,gender,race,age, statusCol = status, timeCol = time, groupCol = , modelVarCols* = gender,race,age, contiCols = age, PLimit = 0.75
case6_strata	properties	survival	(missing)	(missing)	statistics	(missing)
	excludeCol = PatientID,time,status,gender,race,age, statusCol = status, timeCol = time, groupCol = , modelVarCols* = , strataCols = gender, PLimit = 0.75
case7_confInt	properties	survival	(missing)	(missing)	(missing)	(missing)
	statusCol=Event, timeCol=Time, groupCol=Group, confInt=-1

Test case

Parameters▼

IN
survival

IN
annotation

OUT
report

OUT
statistics

OUT
plots

case1

(missing)

timeCol = Followup,
statusCol = Vitalstatus,
groupCol = SNP_Add_Uncommon,
minCount = 60,
timeOutLimit = 30

case2_one_group

timeCol = Followup,
statusCol = Vitalstatus,
confInt = -1,
annotCol = showMe

case3_multiple_plots

timeCol = Followup,
statusCol = Vitalstatus,
groupCol = *,
excludeCol = ID,Dgage,Ageatlastupdate,Foll_20y,Death_20y

case4_plimit

(missing)

timeCol = Followup,
statusCol = Vitalstatus,
groupCol = *,
excludeCol = ID,
PLimit = 0.5,
eventSymbol = 0,
title = Kaplan-Meier test,
xLabel = Ueberlebensdauer

case5_cox

(missing)

excludeCol = PatientID,time,status,gender,race,age,
statusCol = status,
timeCol = time,
groupCol = *,
modelVarCols = gender,race,age,
contiCols = age,
PLimit = 0.75

case6_strata

properties

survival

(missing)

statistics

(missing)

excludeCol = PatientID,time,status,gender,race,age,
statusCol = status,
timeCol = time,
groupCol = *,
modelVarCols = ,
strataCols = gender,
PLimit = 0.75

case7_confInt

properties

survival

(missing)

statusCol=Event,
timeCol=Time,
groupCol=Group,
confInt=-1

Anduril