Fitted-Model-Based Annotations :: Cheat Sheet

Basics

ggpmisc follows the grammar of graphics implemented in ggplot2, based on the idea that many different data visualizations can be built by combining the same components: a data set, a coordinate system, and geoms—visual marks that represent data or summaries derived from data. These elements are complemented by stats that computate data summaries to be passed to geoms and scales that describe the mapping of data into graphical elements.

There are multiple variations of each element of the grammar, providing a vocabulary. Thus, the grammar allows you to ‘speak/write’ a graph from composable elements, instead of being limited to a predefined set of charts. ‘ggpmisc’ adds new stats and scales, expanding the vocabulary while remaining consistent with the grammar.

If you are not already familiar with the grammar of graphics and ggplot2 you should visit the ggplot2 Cheat Sheet first, and afterwards come back to this Cheat Sheet.

Differently to ggplot2, no geometries with the new stats as their default are provided. The plot layers described here are always added with a stat, and when necessary, their default geom argument can be overridden. The default geoms used by the statistics described below are from packages ggplot2 and ggpp.

library(ggpmisc)

Most of the layer functions in ggpmisc aim at making it easier to add to plots information derived from model fitting, tests of significance or statistical summaries. All the stats from ‘ggpmisc’ do computations by data group except for stat_fit_tb() and stat_multcomp() that do computations by plot panel.

The statistics that return predicted values for regressions return x and y where one of the variables is a sequence of numbers for the explanatory variables and the other contains the predictions based on them; depending on the orientation or formula, ymin and ymax, or xmin and xmax, give the lower and upper confidence limits for the fitted line or curve.

The statistics returning fitted or residual values return these values as variables y.fitted or x.fitted, y.resid or x.resid, weights and robustness.weights. Variables x and y contain the observed values. When present, weights are the prior weights, and robustness.weights are posterior weights, those actually used by the model fit function, possibly computed by it.

The statistics that return text labels for annotating plots, return in x and y the label coordinates, the values passed as arguments to parameters label.x and label.y, or values computed based on them. The character strings are returned as variables with names ending in .label. These variables can be used in mappings created with aes() or with use_label(). The difference is that use_label() accepts short names for the labels, recognizes them as computed by the stat and pastes them into a single character string (e.g., use_label("eq", "R2", "n", sep = ", ") is equivalent to aes(paste(after_stat("eq.label"), after_stat("rr.label"), after_stat("n.label), sep = ", "), saving some typing. In most cases numeric values for the parameter estimates are also returned.

Correlation

stat_correlation() computes parametric r or non-parametric correlation coefficients, \tau and \rho, and optionally their confidence intervals, P, and n, the number of observations, flexibly adding an annotation to the plot.

Fitted models

The statistics for fitted models come in matched pairs, one that adds a plot layer with one or more curves and confidence band(s), and one that annotates the plot with the fitted model equation and/or other parameter estimates. These depend on the type of fitted model and include R^2, F, P, AIC, BIC, and n. The curve plotting stats fulfil a similar role to ggplot2::stat_smooth() while the ones for textual annotations have no equivalent in ‘ggplot2’.

stat_poly_line() and stat_poly_line() are the pair supporting a broader set of model fit functions: e.g., linear models (OLS, resistant and robust), general linear model (gls), linear splines, cubic splines, aditive models (gam), major axis (MA) and standardised major axis (SMA) regression, etc. The fitted model equation is automatically generated for polynomials, but can be assembled manually for other model formulas.
stat_quant_line(), stat_quant_band() and stat_quant_eq() support quantile regression based on both polynomials and smoothing splines (using ‘quantreg’).
stat_ma_line() and stat_ma_eq() support major axis (MA), standardised major axis (SMA) and ranged major axis (RMA) regression (using ‘lmodel2’).
stat_fit_augment() works with model fit functions supported by broom::augment() methods including non-linear models. Providing an alternative to stat_poly_line() for a broader range of model fit functions.
stat_fit_tidy() works with model fit functions supported by broom::tidy() methods including non-linear models. Provides numeric values from which labels can be created for a broader range of model fit functions than those suppoerted by stat_poly_eq()
stat_fit_fitted() and stat_fit_deviations() can be used to highlight the fitted values and their distance to the observations in a scatterplot supporting a wide range of model fit functions.
stat_fit_residuals() can be used to create consistent plots of residuals for many different model fit functions supporting a wide range of model fit functions.
stat_distrmix_line() and stat_distrmix_eq() support fitting of univariate Normal-distribution mixture models or a of a single Normal distribution.

ANOVA or summary tables

stat_fit_tb() fits any model supported by a broom::tidy() method. Adds an ANOVA or Summary table. Which columns are included and their naming can be set by the user.

Multiple comparisons

stat_multcomp() fits a model, computes ANOVA and subsequently calls functions from package ‘multcomp’ to test the significance of Tukey, Dunnet or arbitrary sets of pairwise contrasts, with a choice of the adjustment method for the P-values. Significance of differences can be indicated with letters, asterisks or P-values. Sizes of differences are also computed and available for user-assembled labels.

Peaks and valleys

stat_peaks() finds and labels peaks (= global or local maxima).
stat_valleys() finds and labels valleys (= global or local minima).

Volcano and quadrant plots

These plots are frequently used with gene expression data, and each of the many genes labelled based on the ternary outcome from a statistical test. Data are usually, in addition transformed. ‘ggpmisc’ provides several variations on continuous, colour, fill and shape scales, with defaults set as needed. Scales support log fold-change (logFC), false discovery ratio (FDR), P-value (Pvalue) and binary or ternary test outcomes (outcome).

Utility functions

Most of the functions used to generate formatted labels in layers and scales are also exported.

Learn more at docs.r4photobiology.info/ggpmisc/.

‘ggpmisc’ 0.7.0.9000

Pedro J. Aphalo

2026-05-03