Group-comparison Heatmap

Authors

[Editor] Hu Zheng;

[Contributors]

Modified

2026-01-17

Note

Hiplot website

This page is the tutorial for source code version of the Hiplot Group-comparison Heatmap 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/group-comparison?lang=en

Group-comparison Heatmap provides a way to compare multiple variables across multiple (>2) groups and visualize the result with heatmap.

Setup

  • System Requirements: Cross-platform (Linux/MacOS/Windows)

  • Programming language: R

  • Dependent packages: data.table; jsonlite; sigminer

# Install packages
if (!requireNamespace("data.table", quietly = TRUE)) {
  install.packages("data.table")
}
if (!requireNamespace("jsonlite", quietly = TRUE)) {
  install.packages("jsonlite")
}
if (!requireNamespace("sigminer", quietly = TRUE)) {
  remotes::install_github("ShixiangWang/sigminer")
}

# Load packages
library(data.table)
library(jsonlite)
library(sigminer)
sessioninfo::session_info("attached")
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.2 (2025-10-31)
 os       Ubuntu 24.04.3 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       UTC
 date     2026-01-17
 pandoc   3.1.3 @ /usr/bin/ (via rmarkdown)
 quarto   1.8.27 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 Biobase      * 2.70.0  2025-10-29 [1] Bioconduc~
 BiocGenerics * 0.56.0  2025-10-29 [1] Bioconduc~
 data.table   * 1.18.0  2025-12-24 [1] RSPM
 generics     * 0.1.4   2025-05-09 [1] RSPM
 jsonlite     * 2.0.0   2025-03-27 [1] RSPM
 sigminer     * 2.3.1   2024-05-11 [1] RSPM

 [1] /home/runner/work/_temp/Library
 [2] /opt/R/4.5.2/lib/R/site-library
 [3] /opt/R/4.5.2/lib/R/library
 * ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

Data Preparation

# Load data
data <- data.table::fread(jsonlite::read_json("https://hiplot.cn/ui/basic/group-comparison/data.json")$exampleData$textarea[[1]])
data <- as.data.frame(data)

# View data
head(data)
  g1 g2 e1         e2
1  A AA  N -1.8060313
2  A AA  N -0.5820759
3  A AA  N -1.1088896
4  A AA  N -1.0149620
5  A AA  P -0.1623095
6  A AA  N  0.5630558

Visualization

# Define plot functions
unlist_and_covert <- function(x, recursive = FALSE) {
  if (!is.null(x)) {
    x <- unlist(x, recursive = recursive)
    if (!is.null(x)) {
      y <- sapply(x, function(x) {
        if (identical(x, "NA")) NA else x
      })
      names(y) <- names(x)
      x <- y
    }
  }
  x
}

plotentry <- function(data,
                      grp_vars = NULL, enrich_vars = NULL, cross = TRUE,
                      co_method = c("t.test", "wilcox.test"), ref_group = NA,
                      scales = "free", add_text_annotation = TRUE,
                      fill_by_p_value = TRUE, use_fdr = TRUE, cut_p_value = FALSE,
                      cluster_row = FALSE) {
  ref_group <- unlist_and_covert(ref_group)
  if (is.null(ref_group)) ref_group <- NA
  rv <- group_enrichment(data, grp_vars, enrich_vars, cross, co_method, ref_group)
  if (length(unique(rv$grp_var)) == 1) {
    p <- show_group_enrichment(rv,
      return_list = TRUE,
      scales = scales, add_text_annotation = add_text_annotation,
      fill_by_p_value = fill_by_p_value, use_fdr = use_fdr, cut_p_value = cut_p_value,
      cluster_row = cluster_row
    )
    p <- p[[1]]
  } else {
    p <- show_group_enrichment(rv,
      scales = scales, add_text_annotation = add_text_annotation,
      fill_by_p_value = fill_by_p_value, use_fdr = use_fdr, cut_p_value = cut_p_value,
      cluster_row = cluster_row
    )
  }
  return(p)
}

# plot
p <- plotentry(
  data = data,
  grp_vars = "g1",
  enrich_vars = c("e1", "e2"),
  cross = T,
  add_text_annotation = T,
  fill_by_p_value = T,
  use_fdr = T,
  cut_p_value = F,
  cluster_row = F,
  co_method = "t.test",
  scales = "free"
)

p
FigureΒ 1: Group-comparison Heatmap