Nomogram (Logistic)

Authors

[Editor] Hu Zheng;

[Contributors]

Note

Hiplot website

This page is the tutorial for source code version of the Hiplot Nomogram (Logistic) plugin. You can also use the Hiplot website to achieve no code ploting. For more information please see the following link:

https://hiplot.cn/basic/nomogram-logistic?lang=en

Setup

System Requirements: Cross-platform (Linux/MacOS/Windows)
Programming language: R
Dependent packages: rms; ggplotify

# Install packages
if (!requireNamespace("rms", quietly = TRUE)) {
  install.packages("rms")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# Load packages
library(rms)
library(ggplotify)

Data Preparation

# Load data
data <- read.delim("files/Hiplot/130-nomogram-logistic-data.txt", header = T)

# Convert data structure
dd <- datadist(data)
options(datadist = "dd")
## Build Logistic model and run nomogram
logistic_res <- lrm(data=data, as.formula(paste(
    colnames(data)[1], " ~ ",
    paste(colnames(data)[2:length(colnames(data))],
      collapse = "+"
    )
  ))
)
logistic_nomo <- nomogram(logistic_res, maxscale = 100,
  fun= function(x)1/(1+exp(-x)), lp=F, funlabel="Dead Risk",
  fun.at=c(.001,.01,.05,seq(.1,.9,by=.1),.95,.99,.999)
)

# View data
head(data)

  status age sex ph.ecog ph.karno pat.karno meal.cal wt.loss
1      2  74   1       1       90       100     1175      NA
2      2  68   1       0       90        90     1225      15
3      1  56   1       0       90        90       NA      15
4      2  57   1       1       90        60     1150      11
5      2  60   1       0      100        90       NA       0
6      1  74   1       1       50        80      513       0

Visualization

# Nomogram (Logistic)
p <- as.ggplot(function() {
  plot(logistic_nomo,
    scale = 1
  )
  title(main = "Nomogram (Logistic)")
})

p