Package: ggpmisc 0.7.0.9008

ggpmisc: Miscellaneous Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics to locate and tag peaks and valleys and to label plots with the equation of a fitted polynomial model by ordinary least squares, major axis, quantile and robust and resistant regression approaches. Line and model equation for Normal mixture models. Labels for P-value, R^2 or adjusted R^2 or information criteria for fitted models; parametric and non-parametric correlation; ANOVA table or summary table for fitted models as plot insets; annotations for multiple pairwise comparisons with adjusted P-values. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported as well as user-defined wrappers on model fit functions, allowing model selection and conditional labelling. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.

Authors:Pedro J. Aphalo [aut, cre], Kamil Slowikowski [ctb], Samer Mouksassi [ctb]

ggpmisc_0.7.0.9008.tar.gz
ggpmisc_0.7.0.9008.zip(r-4.7)ggpmisc_0.7.0.9008.zip(r-4.6)ggpmisc_0.7.0.9008.zip(r-4.5)
ggpmisc_0.7.0.9008.tgz(r-4.6-any)ggpmisc_0.7.0.9008.tgz(r-4.5-any)
ggpmisc_0.7.0.9008.tar.gz(r-4.7-any)ggpmisc_0.7.0.9008.tar.gz(r-4.6-any)
ggpmisc_0.7.0.9008.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
ggpmisc/json (API)

# Install 'ggpmisc' in R:
install.packages('ggpmisc', repos = c('https://aphalo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aphalo/ggpmisc/issues

Pkgdown/docs site:https://docs.r4photobiology.info

On CRAN:

Conda:

data-analysisdatavizggplot2-annotationsggplot2-statsstatistics

14.06 score 120 stars 18 packages 5.9k scripts 12k downloads 16 mentions 95 exports 50 dependencies

Last updated from:ed38ab657d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK311
source / vignettesOK261
linux-release-x86_64OK362
macos-release-arm64OK245
macos-oldrel-arm64OK247
windows-develOK345
windows-releaseOK373
windows-oldrelOK365
wasm-releaseOK187

Exports:adj_rr_labelbold_labelcheck_output_typecheck_poly_formulacoefs2poly_eqf_use_labelf_value_labelFC_formatFC_nameFC_plainfind_peaksfind_spikesfind_valleysitalic_labelkeep_augmentkeep_glancekeep_tidymean_value_labeloutcome2factorp_value_labelplain_labelpoly2characterr_ci_labelr_labelrr_ci_labelrr_labelS_value_labelscale_color_logFCscale_color_outcomescale_colour_logFCscale_colour_outcomescale_fill_logFCscale_fill_outcomescale_shape_outcomescale_x_FDRscale_x_logFCscale_x_Pvaluescale_y_FDRscale_y_logFCscale_y_Pvaluesd_value_labelse_value_labelsprintf_dmstat_correlationstat_distrmix_areastat_distrmix_eqstat_distrmix_linestat_fit_augmentstat_fit_deviationsstat_fit_fittedstat_fit_glancestat_fit_residualsstat_fit_tbstat_fit_tidystat_ma_eqstat_ma_linestat_multcompstat_peaksstat_poly_eqstat_poly_linestat_quant_bandstat_quant_eqstat_quant_linestat_spikesstat_valleysStatCorrelationStatDistrmixEqStatDistrmixLineStatFitAugmentStatFitDeviationsStatFitFittedStatFitGlanceStatFitResidualsStatFitTbStatFitTidyStatMaEqStatMaLineStatMultcompStatPeaksStatPolyEqStatPolyLineStatQuantBandStatQuantEqStatQuantLineStatSpikesStatValleyssymmetric_limitst_value_labelthreshold2factoruse_labelvalue2charvar_value_labelxy_outcomes2factorxy_thresholds2factorz_value_label

Dependencies:bitopsbootcaToolscliconfintrcpp11dplyrfarvergenericsggplot2ggppgluegridExtragtableisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixMatrixModelspillarpkgconfigplyrpolynompurrrquantregR6RColorBrewerRcpprlangS7scalesSparseMsplus2Rstringistringrsurvivaltibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithrxtszoo

Fitted-Model-Based Annotations
Purpose | Introduction to computed annotations | Statistics | Model equations and other annotations | Fitted lines, confidence bands and residuals | ANOVA and summary tables | Annotations based on package 'broom' | Other data features | Scales | R options | Loading packages | Examples for Statistics | stat_correlation() | stat_poly_eq() and stat_poly_line() | stat_ma_eq() and stat_ma_line() | stat_quant_eq(), stat_quant_line() and stat_quant_band() | stat_distrmix_eq(), stat_distrmix_line() and stat_distrmix_area() | stat_multcomp | stat_fit_residuals | stat_fit_deviations | stat_fit_glance | stat_fit_tb | stat_fit_tidy | stat_fit_augment | Inspecting computed variables and labels | Examples for Scales | scale_color_outcome, scale_fill_outcome | scale_x_FDR, scale_y_FDR, scale_x_logFC, scale_y_logFC, scale_x_Pvalue, scale_y_Pvalue | symmetric_limits | Volcano-plot examples | Quadrant-plot examples

Last update: 2026-06-29
Started: 2016-09-08

Fitted-Model-Based Annotations :: Cheat Sheet
Basics | Correlation | Fitted models | ANOVA or summary tables | Multiple comparisons | Aesthetic mappings | Peaks and valleys | Volcano and quadrant plots | Utility functions

Last update: 2026-06-27
Started: 2025-03-26

Readme and manuals

Help Manual

Help pageTopics
ggpmisc: Miscellaneous Extensions to 'ggplot2'ggpmisc-package ggpmisc
Validate output typecheck_output_type
Validate model formula as a polynomialcheck_poly_formula
Extract Model Coefficientscoef.lmodel2
Format a polynomial as an equationcoefs2poly_eq
Confidence Intervals for Model Parametersconfint.lmodel2
Find local or global maxima (peaks) or minima (valleys)find_peaks find_valleys
Find spikes in vectorfind_spikes
Tidy, glance or augment an object keeping a trace of its originkeep_augment keep_glance keep_tidy
Convert numeric ternary outcomes into a factoroutcome2factor threshold2factor
Format numbers as character labelsadj_rr_label bold_label f_value_label italic_label mean_value_label plain_label p_value_label rr_ci_label rr_label r_ci_label r_label sd_value_label se_value_label S_value_label t_value_label var_value_label z_value_label
Convert a polynomial into character stringpoly2character
Model Predictionspredict.lmodel2
Colour and fill scales for log fold change datascale_color_logFC scale_colour_logFC scale_fill_logFC
Colour and fill scales for ternary outcomesscale_color_outcome scale_colour_outcome scale_fill_outcome
Shape scale for ternary outcomesscale_shape_outcome
Position scales for log fold change datascale_x_logFC scale_y_logFC
Convenience scale for P-valuesscale_x_FDR scale_x_Pvalue scale_y_FDR scale_y_Pvalue
Format numeric values as stringssprintf_dm value2char
Correlation test annotationsstat_correlation
Mixture model prediction and annotationsstat_distrmix_area stat_distrmix_eq stat_distrmix_line
Augment data with fitted values and statisticsstat_fit_augment
Residuals and fitted values from model fitstat_fit_deviations stat_fit_fitted stat_fit_residuals
One row summary data frame for a fitted modelstat_fit_glance
Fitted-model summary and ANOVA tablesstat_fit_tb
One row data frame with fitted parameter estimatesstat_fit_tidy
Model II prediction and annotationsstat_ma_eq stat_ma_line
Labels for pairwise multiple comparisonsstat_multcomp
Local maxima (peaks) or minima (valleys)stat_peaks stat_valleys
Fitted model prediction and annotationsstat_poly_eq stat_poly_line
Quantile regression predictions and annotationsstat_quant_band stat_quant_eq stat_quant_line
Local narrow maxima or minima (spikes)stat_spikes
Swap x and y in a formulaswap_xy
Expand a range to make it symmetricsymmetric_limits
Typeset/format numbers preserving trailing zerostypeset_numbers
Assemble label and map itf_use_label use_label
Convert two numeric ternary outcomes into a factorxy_outcomes2factor xy_thresholds2factor