composition_plot: Compositional plot

In OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data

Compositional plot

Description

Creates a stacked barchart of features. It is possible to both show barcharts for each sample or group them by a categorical variable. The function is compatible with the class omics method composition().

Usage

composition_plot(
  data,
  palette,
  feature_rank,
  title_name = NULL,
  group_by = NULL
)

Arguments

data	A data.frame or data.table.
palette	An object with names and hexcode or color names, see colormap.
feature_rank	A character variable of the feature column.
title_name	A character to set the ggtitle of the ggplot, (Default: NULL).
group_by	A character variable to aggregate the stacked bars by group (Default: NULL).

Value

A ggplot2 object to be further modified

Examples

library("ggplot2")

# Create mock_data as data.frame (data.table is also supported)
mock_data <- data.frame(
  SAMPLE_ID = rep(paste0("Sample", 1:10), each = 5),
  Genus = rep(c("GenusA","GenusB","GenusC","GenusD","GenusE"), times = 10),
  value = c(
    0.1119, 0.1303, 0.0680, 0.5833, 0.1065,      # Sample1
    0.2080, 0.1179, 0.0211, 0.4578, 0.1951,      # Sample2
    0.4219, 0.1189, 0.2320, 0.1037, 0.1235,      # Sample3
    0.4026, 0.0898, 0.1703, 0.1063, 0.2309,      # Sample4
    0.1211, 0.0478, 0.5721, 0.1973, 0.0618,      # Sample5
    0.2355, 0.0293, 0.2304, 0.1520, 0.3528,      # Sample6
    0.2904, 0.0347, 0.3651, 0.0555, 0.2544,      # Sample7
    0.4138, 0.0299, 0.0223, 0.4996, 0.0345,      # Sample8
    0.4088, 0.0573, 0.0155, 0.2888, 0.2296,      # Sample9
    0.4941, 0.0722, 0.2331, 0.1023, 0.0983       # Sample10
  ),
  Group = rep(c("Group1","Group2","Group1",
                "Group1","Group2","Group2",
                 "Group1","Group1","Group1","Group2"),
               each = 5)
)

# Create a colormap
mock_palette <- c(
  GenusA = "#1f77b4",  # blue
  GenusB = "#ff7f0e",  # orange
  GenusC = "#2ca02c",  # green
  GenusD = "#d62728",  # red
  GenusE = "#9467bd"   # purple
)

# Optionally: Use OmicFlow::colormap()
mock_palette <- colormap(
  data = mock_data,
  col_name = "Genus",
  Brewer.palID = "RdYlBu"
)

composition_plot(
  data = mock_data,
  palette = mock_palette,
  feature_rank = "Genus",
  title_name = "Mock Genus Composition"
)

composition_plot(
  data = mock_data,
  palette = mock_palette,
  feature_rank = "Genus",
  title_name = "Mock Genus Composition by Group",
  group_by = "Group"
)

OmicFlow documentation built on Sept. 9, 2025, 5:24 p.m.