Package 'ggrisk' reference manual

Title:	Risk Score Plot for Cox Regression
Description:	The risk plot may be one of the most commonly used figures in tumor genetic data analysis. We can conclude the following two points: Comparing the prediction results of the model with the real survival situation to see whether the survival rate of the high-risk group is lower than that of the low-level group, and whether the survival time of the high-risk group is shorter than that of the low-risk group. The other is to compare the heat map and scatter plot to see the correlation between the predictors and the outcome.
Authors:	Jing Zhang [aut, cre], Zhi Jin [aut]
Maintainer:	Jing Zhang <[email protected]>
License:	GPL-2
Version:	1.3
Built:	2024-12-11 07:28:38 UTC
Source:	CRAN

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)
)
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))

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))

ICGC Liver Data from Japan

Description

This data is a liver cancer data from Japan Data released in ICGC database (Link). It cantains time, event and four genes.

Usage

data(LIRI)
data(LIRI)

Format

An object of class data.frame with 232 rows and 6 columns.

Examples

data(LIRI)
data(LIRI)

Two Scatter Plot Plot for Cox Regression

Description

Two Scatter Plot Plot for Cox Regression

Usage

two_scatter(
  fit,
  new.data = NULL,
  code.0 = "Alive",
  code.1 = "Dead",
  code.highrisk = "High",
  code.lowrisk = "Low",
  cutoff.show = TRUE,
  cutoff.value = "median",
  cutoff.x,
  cutoff.y,
  cutoff.label,
  title.A.ylab = "Risk Score",
  title.B.ylab = "Survival Time",
  title.xlab = "Rank",
  title.A.legend = "Risk Group",
  title.B.legend = "Status",
  size.AB = 1.5,
  size.ylab.title = 14,
  size.xlab.title = 14,
  size.Atext = 11,
  size.Btext = 11,
  size.xtext = 11,
  size.xyticks = 0.5,
  size.xyline = 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"),
  vjust.A.ylab = 1,
  vjust.B.ylab = 2,
  family = "sans",
  expand.x = 3
)
two_scatter(
  fit,
  new.data = NULL,
  code.0 = "Alive",
  code.1 = "Dead",
  code.highrisk = "High",
  code.lowrisk = "Low",
  cutoff.show = TRUE,
  cutoff.value = "median",
  cutoff.x,
  cutoff.y,
  cutoff.label,
  title.A.ylab = "Risk Score",
  title.B.ylab = "Survival Time",
  title.xlab = "Rank",
  title.A.legend = "Risk Group",
  title.B.legend = "Status",
  size.AB = 1.5,
  size.ylab.title = 14,
  size.xlab.title = 14,
  size.Atext = 11,
  size.Btext = 11,
  size.xtext = 11,
  size.xyticks = 0.5,
  size.xyline = 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"),
  vjust.A.ylab = 1,
  vjust.B.ylab = 2,
  family = "sans",
  expand.x = 3
)

Arguments

`fit`	cox regression results of coxph() from 'survival' package or cph() from 'rms' package
`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 'Riskscore'
`title.B.ylab`	string, y-lab title for figure B. Default is 'Survival Time'
`title.xlab`	string, x-lab title for figure B. Default is 'Rank'
`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'
`size.AB`	numeric, size for ABC. Default is 1.5
`size.ylab.title`	numeric, size for y-axis label title. Default is 14
`size.xlab.title`	numeric, size for x-axis lab title. Default is 11
`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.xtext`	numeric, size for x-axis text. Default is 11
`size.xyticks`	numeric, size for y-axis ticks. Default is 0.5
`size.xyline`	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'
`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

Value

A riskscore picture

Examples

library(rms)
fit <- cph(Surv(time,status)~ANLN+CENPA+GPR182+BCO2,LIRI)
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5)

#more detailed example
library(ggrisk)
#plot
two_scatter(fit)
#regulate cutoff
##hidden cutoff
two_scatter(fit,
            cutoff.show = FALSE)
two_scatter(fit,
            cutoff.value = 'median')
two_scatter(fit,
            cutoff.value = 'roc')
two_scatter(fit,
            cutoff.value = 'cutoff')
two_scatter(fit,
            cutoff.value = -1)
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5)
#code for 0 and 1
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead')
#code for high and low risk group
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group')
#title for legend, x and y lab
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank')
#vertical just for y-axis lab
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3)
#size
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3,
            size.AB = 2,
            size.ylab.title = 14,
            size.xlab.title = 14,
            size.Atext = 12,
            size.Btext = 12,
            size.xtext = 12,
            size.xyticks = 0.5,
            size.xyline = 0.5,
            size.dashline = 1.5,
            size.points = 1,
            size.cutoff = 5,
            size.legendtitle = 14,
            size.legendtext = 13)
#color
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3,
            size.AB = 2,
            size.ylab.title = 14,
            size.xlab.title = 14,
            size.Atext = 12,
            size.Btext = 12,
            size.xtext = 12,
            size.xyticks = 0.5,
            size.xyline = 0.5,
            size.dashline = 1.5,
            size.points = 1,
            size.cutoff = 5,
            size.legendtitle = 14,
            size.legendtext = 13,
            color.A = c(low='green',high='red'),
            color.B = c(code.0='green',code.1='red'))
#famli and expand
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3,
            size.AB = 2,
            size.ylab.title = 14,
            size.xlab.title = 14,
            size.Atext = 12,
            size.Btext = 12,
            size.xtext = 12,
            size.xyticks = 0.5,
            size.xyline = 0.5,
            size.dashline = 1.5,
            size.points = 1,
            size.cutoff = 5,
            size.legendtitle = 14,
            size.legendtext = 13,
            color.A = c(low='green',high='red'),
            color.B = c(code.0='green',code.1='red'),
            family = 'sans', # sans for Arail, serif for Times New Roman
            expand.x=10)

library(rms)
fit <- cph(Surv(time,status)~ANLN+CENPA+GPR182+BCO2,LIRI)
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5)

#more detailed example
library(ggrisk)
#plot
two_scatter(fit)
#regulate cutoff
##hidden cutoff
two_scatter(fit,
            cutoff.show = FALSE)
two_scatter(fit,
            cutoff.value = 'median')
two_scatter(fit,
            cutoff.value = 'roc')
two_scatter(fit,
            cutoff.value = 'cutoff')
two_scatter(fit,
            cutoff.value = -1)
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5)
#code for 0 and 1
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead')
#code for high and low risk group
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group')
#title for legend, x and y lab
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank')
#vertical just for y-axis lab
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3)
#size
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3,
            size.AB = 2,
            size.ylab.title = 14,
            size.xlab.title = 14,
            size.Atext = 12,
            size.Btext = 12,
            size.xtext = 12,
            size.xyticks = 0.5,
            size.xyline = 0.5,
            size.dashline = 1.5,
            size.points = 1,
            size.cutoff = 5,
            size.legendtitle = 14,
            size.legendtext = 13)
#color
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3,
            size.AB = 2,
            size.ylab.title = 14,
            size.xlab.title = 14,
            size.Atext = 12,
            size.Btext = 12,
            size.xtext = 12,
            size.xyticks = 0.5,
            size.xyline = 0.5,
            size.dashline = 1.5,
            size.points = 1,
            size.cutoff = 5,
            size.legendtitle = 14,
            size.legendtext = 13,
            color.A = c(low='green',high='red'),
            color.B = c(code.0='green',code.1='red'))
#famli and expand
two_scatter(fit,
            cutoff.value = 'median',
            cutoff.x = 142,
            cutoff.y = -0.5,
            code.0 = 'Still Alive',
            code.1 = 'Dead',
            code.highrisk = 'High Group',
            code.lowrisk = 'Low Group',
            title.A.legend = 'Riskscore',
            title.B.legend = 'Event Status',
            title.A.ylab = 'Riskscore',
            title.B.ylab = 'Survival Time(year)',
            title.xlab = 'This is rank',
            vjust.A.ylab = 1,
            vjust.B.ylab = 3,
            size.AB = 2,
            size.ylab.title = 14,
            size.xlab.title = 14,
            size.Atext = 12,
            size.Btext = 12,
            size.xtext = 12,
            size.xyticks = 0.5,
            size.xyline = 0.5,
            size.dashline = 1.5,
            size.points = 1,
            size.cutoff = 5,
            size.legendtitle = 14,
            size.legendtext = 13,
            color.A = c(low='green',high='red'),
            color.B = c(code.0='green',code.1='red'),
            family = 'sans', # sans for Arail, serif for Times New Roman
            expand.x=10)

Package 'ggrisk'

Help Index

Risk Score Plot for Cox Regression

Description

Usage

Arguments

Value

Examples

ICGC Liver Data from Japan

Description

Usage

Format

Examples

Two Scatter Plot Plot for Cox Regression

Description

Usage

Arguments

Value

Examples