MKMplot {signatureSurvival}

Multivariate Kaplan-Meier survival curve plot

Description

Function MKMplot plots the outcome of multivariate survival analysis of patients in a cohort. Independent variable is specified as a gene or a signature. Covariates are sex, age, stage, genotype etc. If user needs one or multiple covariates, for example,smoking, tumor stage, etc., user can use X to specify the covariates.

Usage

MKMplot(data, mol, X, HR="hazard risk",time = "month", status = "status", 
sml="hv",quant=c("No",-0.2,0.2),plotmethod="plot",adjx)

Arguments

data

survival data including clinical data such as status, month, age, sex and/or smoking and expression data of genes or signatures.

mol

char value specified a gene symbol or a gene id or a signature existed in data or int value for a column number of a specified gene or a signature in data.

X

a string or string vector for one or multiple specified covariates. For example, X="smoking" or X=c("age","sex",smoking","genotype"). 10 covariates are limited in the current version. All covariates should be listed in the data.

HR

a string to specify hazard risk or hazard rate. If HR="Hazard risk" or "Hazard_risk", then plot would show coefficient, which has negative, zero, or positive value. The domain is (-\infty,\infty). The Negative value indicates reduction of hazard risk while the positive value suggests increment of risk. Zero suggests no change of hazard risk. If HR = "hazard rate" or "hazard_rate", then plot would show exp(coefficient), which the value is from 0 to \infty and HR < 1 indicates that hazard risk is reduced and HR > 1 means that hazard risk is increased. The default is "hazard risk". HR is only used in plot.

time

string for survival time and may be one of c("day", "month", "year"), depending on the clinical data. The default value is "month".

status

string to specify status name in the input survival data. For example, status may be "death", "relapse", or "status", depending on user's data. The default value is "status".

sml

surv.median.line: character vector for drawing a horizontal/vertical line at median survival. Allowed values include one of c("none", "hv", "h", "v"). v: vertical, h:horizontal. The value of sml is used in only ggsurvplot. The default is "hv".

quant

vector for quantile, low and high values. the low and high values are used to define or classify low and high expression groups. If quantile is "yes" or "YES", then the low and high are non-negative precent values, for example, quant=c("yes",0.25,0.75). If quantile is "no", then the low and high values are z-scores, the low value may be negative. For example, quant=c("no",-0.2, 0.2). The quantile = "yes" or = "No" may produce different results of survival analysis. User should carefully choose qunatile or no quantile according to the data. The default values are c("no",-0.2,0.2).

plotmethod

string value: choose a method to plot Kaplan-Meier survival curves. In current version, we have two methods for chose: plot and ggsurvplot. The defauld is plot method. In plot method, we show p-value for result of Ward t-test but in ggsurvplot, we show p-value for the result of log-rank test.

adjx

numeric value used to adjust x-axis position of p-value and HR in only plot.

Details

survival data contain clinical data such as status, month, age, sex and/or smoking and expression of gene or protein. The status may be death, recurrence or relapse and must be a binary variable: 1 for an event (such as death) or 0 for no event (such as alive). The month, age, and gene are numeric continuous variables but sex is a binary variable. The other covariates may be numeric continuous or binary variables. They are listed in column and patients or observations are listed in row.

Value

output a survival curve plot of multivariate survival analysis.

Note

To plot outcome of univariate survival, user can use UKMplot. All inputting parametes are not sensitive to upper or lower. That is, user can input upper or lower string or letter. For example, both time ="MONTH" or time = "month" work.

Author(s)

Yuan-De Tan
[e-mail]
[e-mail]
Yuguang Ban
[e-mail]

See Also

UKMplot,MUKMplot,MMKMplot

Examples

require(survival)
require(ggplot2)
data(GSE50081)
MKMplot(data=GSE50081,mol=56,X=c("t.stage","n.stage",	"m.stage"),time="month",
status="status1",sml="none",quant=c("No",-0.2,0.2),plotmethod="ggsurvplot",
adjx = 5)