ggrisk {ggrisk} | R Documentation |
Risk Score Plot for Cox Regression
Description
Risk Score Plot for Cox Regression
Usage
ggrisk(
fit,
heatmap.genes = NULL,
new.data = NULL,
code.0 = "Alive",
code.1 = "Dead",
code.highrisk = "High",
code.lowrisk = "Low",
cutoff.show = TRUE,
cutoff.value = "median",
cutoff.x = NULL,
cutoff.y = NULL,
cutoff.label = NULL,
title.A.ylab = "Risk Score",
title.B.ylab = "Survival Time",
title.A.legend = "Risk Group",
title.B.legend = "Status",
title.C.legend = "Expression",
size.ABC = 1.5,
size.ylab.title = 14,
size.Atext = 11,
size.Btext = 11,
size.Ctext = 11,
size.yticks = 0.5,
size.yline = 0.5,
size.points = 2,
size.dashline = 1,
size.cutoff = 5,
size.legendtitle = 13,
size.legendtext = 12,
color.A = c(low = "blue", high = "red"),
color.B = c(code.0 = "blue", code.1 = "red"),
color.C = c(low = "blue", median = "white", high = "red"),
vjust.A.ylab = 1,
vjust.B.ylab = 2,
family = "sans",
expand.x = 3,
relative_heights = c(0.1, 0.1, 0.01, 0.15)
)
Arguments
fit |
cox regression results of coxph() from 'survival' package or cph() from 'rms' package |
heatmap.genes |
(optional) numeric variables. Name for genes |
new.data |
new data for validation |
code.0 |
string. Code for event 0. Default is 'Alive' |
code.1 |
string. Code for event 1. Default is 'Dead' |
code.highrisk |
string. Code for highrisk in risk score. Default is 'High' |
code.lowrisk |
string. Code for lowrisk in risk score. Default is 'Low' |
cutoff.show |
logical, whether to show text for cutoff in figure A. Default is TRUE |
cutoff.value |
string, which can be 'median', 'roc' or 'cutoff'. Even you can define it by yourself |
cutoff.x |
numeric (optional), ordination x for cutoff text |
cutoff.y |
numeric (optional), ordination y for cutoff text |
cutoff.label |
(should be) string. Define cutoff label by yourself |
title.A.ylab |
string, y-lab title for figure A. Default is 'Risk Score' |
title.B.ylab |
string, y-lab title for figure B. Default is 'Survival Time' |
title.A.legend |
string, legend title for figure A. Default is 'Risk Group' |
title.B.legend |
string, legend title for figure B. Default is 'Status' |
title.C.legend |
string, legend title for figure C. Default is 'Expression' |
size.ABC |
numeric, size for ABC. Default is 1.5 |
size.ylab.title |
numeric, size for y-axis label title. Default is 14 |
size.Atext |
numeric, size for y-axis text in figure A. Default is 11 |
size.Btext |
numeric, size for y-axis text in figure B. Default is 11 |
size.Ctext |
numeric, size for y-axis text in figure C. Default is 11 |
size.yticks |
numeric, size for y-axis ticks. Default is 0.5 |
size.yline |
numeric, size for y-axis line. Default is 0.5 |
size.points |
numeric, size for scatter points. Default is 2 |
size.dashline |
numeric, size for dashline. Default is 1 |
size.cutoff |
numeric, size for cutoff text. Default is 5 |
size.legendtitle |
numeric, size for legend title. Default is 13 |
size.legendtext |
numeric, size for legend text. Default is 12 |
color.A |
color for figure A. Default is low = 'blue', high = 'red' |
color.B |
color for figure B. Default is code.0 = 'blue', code.1 = 'red' |
color.C |
color for figure C. Default is low = 'blue', median = 'white', high = 'red' |
vjust.A.ylab |
numeric, vertical just for y-label in figure A. Default is 1 |
vjust.B.ylab |
numeric, vertical just for y-label in figure B. Default is 2 |
family |
family, default is sans |
expand.x |
numeric, expand for x-axis |
relative_heights |
numeric, relative heights for figure A, B, colored side bar and heatmap. Default is 0.1 0.1 0.01 and 0.15 |
Value
A risk score picture
Examples
library(rms)
library(ggrisk)
fit <- cph(Surv(time,status)~ANLN+CENPA+GPR182+BCO2,LIRI)
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8)
#more detailed example
#plot
ggrisk(fit)
#heatmap.genes
ggrisk(fit,
heatmap.genes=c('GPR182','CENPA','BCO2'))
#cutoff
ggrisk(fit,
cutoff.value='median') #default
ggrisk(fit,
cutoff.value='roc')
ggrisk(fit,
cutoff.value='cutoff')
ggrisk(fit,
cutoff.value=-1)
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8)
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
cutoff.label='This is cutoff')
#code for 0 and 1
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead')
#code for high and low risk group
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead',
code.highrisk = 'High Risk',
code.lowrisk = 'Low Risk')
#title
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead',
code.highrisk = 'High Risk',
code.lowrisk = 'Low Risk',
title.A.ylab='Risk Score',
title.B.ylab='Survival Time(year)',
title.A.legend='Risk Group',
title.B.legend='Status',
title.C.legend='Expression')
#size
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead',
code.highrisk = 'High Risk',
code.lowrisk = 'Low Risk',
title.A.ylab='Risk Score',
title.B.ylab='Survival Time(year)',
title.A.legend='Risk Group',
title.B.legend='Status',
title.C.legend='Expression',
size.ABC=1.5,
size.ylab.title=14,
size.Atext=11,
size.Btext=11,
size.Ctext=11,
size.yticks=0.5,
size.yline=0.5,
size.points=2,
size.dashline=1,
size.cutoff=5,
size.legendtitle=13,
size.legendtext=12)
#color
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead',
code.highrisk = 'High Risk',
code.lowrisk = 'Low Risk',
title.A.ylab='Risk Score',
title.B.ylab='Survival Time(year)',
title.A.legend='Risk Group',
title.B.legend='Status',
title.C.legend='Expression',
size.ABC=1.5,
size.ylab.title=14,
size.Atext=11,
size.Btext=11,
size.Ctext=11,
size.yticks=0.5,
size.yline=0.5,
size.points=2,
size.dashline=1,
size.cutoff=5,
size.legendtitle=13,
size.legendtext=12,
color.A=c(low='blue',high='red'),
color.B=c(code.0='blue',code.1='red'),
color.C=c(low='blue',median='white',high='red'))
#vjust
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead',
code.highrisk = 'High Risk',
code.lowrisk = 'Low Risk',
title.A.ylab='Risk Score',
title.B.ylab='Survival Time(year)',
title.A.legend='Risk Group',
title.B.legend='Status',
title.C.legend='Expression',
size.ABC=1.5,
size.ylab.title=14,
size.Atext=11,
size.Btext=11,
size.Ctext=11,
size.yticks=0.5,
size.yline=0.5,
size.points=2,
size.dashline=1,
size.cutoff=5,
size.legendtitle=13,
size.legendtext=12,
color.A=c(low='blue',high='red'),
color.B=c(code.0='blue',code.1='red'),
color.C=c(low='blue',median='white',high='red'),
vjust.A.ylab=1,
vjust.B.ylab=2)
#family, expand, relative height
ggrisk(fit,
cutoff.value='median',
cutoff.x = 145,
cutoff.y = -0.8,
code.0 = 'Still Alive',
code.1 = 'Already Dead',
code.highrisk = 'High Risk',
code.lowrisk = 'Low Risk',
title.A.ylab='Risk Score',
title.B.ylab='Survival Time(year)',
title.A.legend='Risk Group',
title.B.legend='Status',
title.C.legend='Expression',
size.ABC=1.5,
size.ylab.title=14,
size.Atext=11,
size.Btext=11,
size.Ctext=11,
size.yticks=0.5,
size.yline=0.5,
size.points=2,
size.dashline=1,
size.cutoff=5,
size.legendtitle=13,
size.legendtext=12,
color.A=c(low='blue',high='red'),
color.B=c(code.0='blue',code.1='red'),
color.C=c(low='blue',median='white',high='red'),
vjust.A.ylab=1,
vjust.B.ylab=2,
family='sans',
expand.x=3,
relative_heights=c(0.1,0.1,0.01,0.15))