UKMplot {signatureSurvival}

Univariate Kaplan-Meier survival curve plot

Description

Function UKMplot is used to plot outcome of survival analysis of patients in a cohort using a specified gene or a signature.

Usage

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

Arguments

data

survival data in which columns contain patient survival data such as survival status, survival month, age, sex,cell type and genes and rows list all patients. Status and sex are binary data. In status, 1 is defined as an event occurrece (such as death) and 0 as no event occurrence (such as alive). Month, age, and genes, signature are numeric and continuous data.

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 signature in 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.

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 for survival status of patients, may be "relapse" or "recurrence" or "death". User can set status="death", "relapse" or "recurrence","status" depending on user's survival 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 ggsurvplot, not in plot. 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 chose: plot and ggsurvplot. The defauld is plot method

adjx

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

Details

UKMplot is a function invoked by MKMplot. By invoking UMKplot, MKMplot can make a set of survival plots for a set of genes or a set of signatures.

Value

outputs a survival curve plot of a specified gene.

Note

For a multivariate survival analysis, user can use MVKMplot to plot survival outcome.

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

MKMplot,MMKMplot,MUKMplot

Examples

require(survival)
require(ggplot2)
data(TCGA_survivalData)
UKMplot(data=TCGA_survivalData,mol=78,time="month", status="status",
quant=c("No",-0.2,0.2),adjx=100)
UKMplot(data=TCGA_survivalData,mol="RPS28",time="month", status="status",adjx=100)