MMKMplot {signatureSurvival}

Multiple multivariate Kaplan-Meier survival curve plots

Description

Function MMKMplot plots outcomes of multivariate survival analyses of patients with covariates age and sex in a cohort with a specified set of genes. Each gene has a plot and each plot takes a page.

Usage

MMKMplot(sdata, stn, gn, X, HR="hazard risk", status = "status", 
time = "month", sml="hv",quant=c("No",-0.2,0.2),plotmethod="plot",adjx,
outdir, file)

Arguments

sdata

survival data including clinical data such as status, month, age, sex, and expressions of genes or expressions of proteins. Status such as death, recurrence or relapse must be 1 for event (such as death) or 0 for no event (such as alive), month is numeric data, age is numeric data, sex is binary data and genes are numeric data. They are listed in columns and patients are listed in rows.

stn

character value specifying gene symbol or gene id existed in sdata or int value specifying column number for the first gene in survival data.

gn

character value specifying gene symbol or gene id existed in sdata or int value specifying column number for the last gene in survival data.

X

string vector for covariate(s), an option with inputting names of one, two, three or more covariates. For example, X="smoking", X=c("age","sex","smoking","stage_n" ). The number of covariates is limited to 10. All covariates should be listed in the data.

HR

a string for specifying 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.

status

string for a specifying status name. For example, status may be death, relapse or recurrence. User can set status="death", "relapse" or "recurrence" or "status", depending on the data.

time

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

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 quantile 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 choice: 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-sum test.

adjx

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

outdir

string, a path to save a file. If user uses setwd to set a dir for saving file, the outdir can be set "NULL", MMKMplot can automatically save pdf file in this dir folder in user local computer.

file

string for file name. If user sets a path with setwd or a path to outdir, then file just sets file name. The file is a pdf file containing all plot pages.

Value

output multiple pdf pages for multiple survival curve plots and saved in a outputting pdf file. If file ="NULL", MUKMplot would output the last survival plot page.

Note

User may not perform this function if unnecessary.

All inputting parameters 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,MKMplot,MUKMplot

Examples

data(GSE50081)
XX=c("age","sex","t.stage","n.stage","m.stage")
hr="hazard rate"

MMKMplot(sdata=GSE50081,stn="X232578_at", gn="down",X=XX,HR=hr,status="status1", 
time="month", quant=c("yes",0.25,0.75),plotmethod="plot",adjx = 3.5,file =
"NULL")