ggrisk
Risk Score Plot for Cox Regression

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ggrisk: Risk Score Plot for Cox Regression

ggrisk: Risk Score Plot for Cox Regression
In ggrisk: Risk Score Plot for Cox Regression

Description Usage Arguments Value Examples

View source: R/ggrisk.R

Description

Risk Score Plot for Cox Regression

Usage

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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

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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))

ggrisk documentation built on Aug. 9, 2021, 9:12 a.m.

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