Parallel Coordinate

Authors

[Editor] Hu Zheng;

[Contributors]

Note

Hiplot website

This page is the tutorial for source code version of the Hiplot Parallel Coordinate 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/parallel-coordinate?lang=en

Setup

System Requirements: Cross-platform (Linux/MacOS/Windows)
Programming language: R
Dependent packages: GGally; hrbrthemes; viridis; ggthemes

# Install packages
if (!requireNamespace("GGally", quietly = TRUE)) {
  install.packages("GGally")
}
if (!requireNamespace("hrbrthemes", quietly = TRUE)) {
  install.packages("hrbrthemes")
}
if (!requireNamespace("viridis", quietly = TRUE)) {
  install.packages("viridis")
}
if (!requireNamespace("ggthemes", quietly = TRUE)) {
  install.packages("ggthemes")
}

# Load packages
library(GGally)
library(hrbrthemes)
library(viridis)
library(ggthemes)

Data Preparation

# Load data
data <- read.delim("files/Hiplot/132-parallel-coordinate-data.txt", header = T)

# Convert data structure
data[, 6] <- factor(data[, 6], levels = unique(data[, 6]))

# View data
head(data)

    Name Value1 Value2 Value3 Value4       Group
1    ATR    5.1    3.5    1.4    0.2 p53 pathway
2  CHEK1    4.9    3.0    1.4    0.2 p53 pathway
3  GORAB    4.7    3.2    1.3    0.2 p53 pathway
4 CDKN2A    4.6    3.1    1.5    0.2 p53 pathway
5   MDM2    5.0    3.6    1.4    0.2 p53 pathway
6   MDM4    5.4    3.9    1.7    0.4 p53 pathway

Visualization

# Parallel Coordinate
p <- ggparcoord(data, columns = 2:(ncol(data) - 1), groupColumn = ncol(data),
                title = "Parallel Coordinate Plot for cancer Data",
                alphaLines = 0.3, scale = "globalminmax",
                showPoints = T, boxplot = F) +
  theme_base() +
  theme(text = element_text(family = "Arial"),
        plot.title = element_text(size = 12, hjust = 0.5),
        axis.title = element_text(size = 10),
        axis.text = element_text(size = 12),
        axis.text.x = element_text(angle = 0, hjust = 0.5,vjust = 1),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10)) +
  scale_color_viridis(discrete = TRUE) +
  facet_grid(formula(paste("~", (colnames(data)[ncol(data)]))))

p