ggrisk: Risk Score Plot for Cox Regression

In yikeshu0611/TCGAimmunelncRNA: TCGAimmunelncRNA

Description

Risk Score Plot for Cox Regression

Usage

ggrisk(
  fit,
  heatmap.genes = NULL,
  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
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

yikeshu0611/TCGAimmunelncRNA documentation built on Dec. 23, 2021, 7:20 p.m.