R/ggplot2-based modular scientific plotting framework with automatic statistical diagnostics.
Fplot is a publication-ready scientific plotting system designed for plant biology research. It provides 13 chart types with automatic statistical analysis, following the Fv1.4 color and formatting specification.
| Code | Type | Function |
|---|---|---|
| A01 | Simple bar plot | plot_simple_barplot() |
| A02 | Grouped bar plot | plot_grouped_barplot() |
| A03 | Stacked bar plot | plot_stacked_barplot() |
| B01 | Simple box plot | plot_simple_boxplot() |
| B02 | Grouped box plot | plot_grouped_boxplot() |
| B03 | Simple violin plot | plot_simple_violin() |
| B04 | Grouped violin plot | plot_grouped_violin() |
| C01 | Simple line plot | plot_simple_lineplot() |
| D01 | Fitted scatter plot | plot_fitted_scatter() |
| D02 | Correlation scatter plot | plot_cor_scatter() |
| D03 | PCA density plot | plot_pca_density() |
| Z01 | IMATE combined heatmap | plot_imate() |
| Z02 | Correlation heatmap | plot_heatmap() |
# 1. Load configuration
setwd("path/to/Fplot")
source("config/global_settings.R", encoding = "UTF-8")
source("scripts/stat_utils.R", encoding = "UTF-8")
# 2. Load plot script
source("scripts/Fplot-B01.R", encoding = "UTF-8")
# 3. Read data and plot
df <- read.csv("datasample/datasample.csv")
plot_simple_boxplot(data = df, x_col = "group", y_col = "value")- Automatic statistical diagnostics: Shapiro-Wilk normality → Levene homogeneity → parametric/non-parametric selection
- Smart significance annotation: 2-3 groups → bracket; ≥4 groups → CLD (Compact Letter Display)
- Two-way ANOVA support: Interaction effects + simple main effects (A02/B02/B04)
- Fv1.4 color specification: OE red (#B2182B), CR blue (#2166AC), neutral gray (#999999)
- Publication-ready output: 300 DPI, PNG/PDF/SVG, Arial font, standardized dimensions
Fplot/
├── SKILL.md # Skill definition (for MoLiLi/WorkBuddy)
├── README.md # This file
├── config/ # Global settings
│ ├── global_settings.R
│ ├── color_palettes.R
│ ├── theme_F.R
│ └── stat_settings.R
├── scripts/ # Plot scripts (latest version only)
│ ├── stat_utils.R
│ ├── Fplot-A01.R ... Fplot-Z02.R
├── datasample/ # Test datasets
├── templates/ # Data format templates
├── docs/ # Documentation & examples
│ ├── Fplot-go.md
│ └── examples/
└── output/ # Generated at runtime
- R ≥ 4.5.0
- Packages: ggplot2, dplyr, tidyr, ggsignif, car, rstatix, multcompView, FSA (optional), linkET, psych, aplot, readxl, reshape2, stringr, ggtext
MIT License
If you use Fplot in your research, please cite:
FangLab Fplot: A modular scientific plotting framework for R/ggplot2. (2026)