Description Usage Arguments Value Examples
Two Scatter Plot Plot for Cox Regression
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | 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
)
|
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 |
A riskscore picture
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.