Package: ggpmisc 0.6.1

ggpmisc: Miscellaneous Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. 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]

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ggpmisc.pdf |ggpmisc.html✨
ggpmisc/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://docs.r4photobiology.info

On CRAN:

data-analysisdatavizggplot2-annotationsggplot2-statsstatistics

13.39 score 102 stars 13 packages 4.2k scripts 18k downloads 16 mentions 84 exports 57 dependencies

Last updated 30 days agofrom:b3c0460e1e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-winOKDec 13 2024
R-4.5-linuxOKDec 13 2024
R-4.4-winOKDec 13 2024
R-4.4-macOKDec 13 2024
R-4.3-winOKDec 13 2024
R-4.3-macOKDec 13 2024

Exports:adj_rr_labelbold_labelcheck_poly_formulacoefs2poly_eqf_value_labelFC_formatFC_nameFC_plainfind_peaksitalic_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_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_valleysStatCorrStatFitAugmentStatFitDeviationsStatFitFittedStatFitGlanceStatFitResidualsStatFitTbStatFitTidyStatMaEqStatMaLineStatMultcompStatPeaksStatPolyEqStatPolyLineStatQuantBandStatQuantEqStatQuantLineStatValleyssymmetric_limitst_value_labelthreshold2factoruse_labelvalue2charvar_value_labelxy_outcomes2factorxy_thresholds2factorz_value_label

Dependencies:bootclicodetoolscolorspaceconfintrcpp11dplyrfansifarvergenericsggplot2ggppgluegridExtragtableisobandlabelinglatticelifecyclelmodel2lubridatemagrittrMASSMatrixMatrixModelsmgcvmultcompmultcompViewmunsellmvtnormnlmepillarpkgconfigplyrpolynomquantregR6RColorBrewerRcpprlangsandwichscalesSparseMsplus2RstringistringrsurvivalTH.datatibbletidyselecttimechangeutf8vctrsviridisLitewithrxtszoo

Fitted-Model-Based Annotations

Pedro J. Aphalo

Rendered frommodel-based-annotations.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-06-01
Started: 2021-01-18

Readme and manuals

Help Manual

Help pageTopics
ggpmisc: Miscellaneous Extensions to 'ggplot2'ggpmisc-package ggpmisc
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 maxima or global maximum (peaks)find_peaks
Tidy, glance or augment an object keeping a trace of its originkeep_augment keep_glance keep_tidy
Moved to package 'gginnards'append_layers bottom_layer delete_layers extract_layers geom_debug geom_null Moved move_layers num_layers shift_layers stat_debug_group stat_debug_panel top_layer which_layers
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
Annotate plot with correlation teststat_correlation
Augment data with fitted values and statisticsstat_fit_augment
Residuals from model fit as segmentsstat_fit_deviations stat_fit_fitted
One row summary data frame for a fitted modelstat_fit_glance
Residuals from a model fitstat_fit_residuals
Model-fit summary or ANOVAstat_fit_tb
One row data frame with fitted parameter estimatesstat_fit_tidy
Equation, p-value, R^2 of major axis regressionstat_ma_eq
Predicted line from major axis linear fitstat_ma_line
Labels for pairwise multiple comparisonsstat_multcomp
Local maxima (peaks) or minima (valleys)stat_peaks stat_valleys
Equation, p-value, R^2, AIC and BIC of fitted polynomialstat_poly_eq
Predicted line from linear model fitstat_poly_line
Predicted band from quantile regression fitsstat_quant_band
Equation, rho, AIC and BIC from quantile regressionstat_quant_eq
Predicted line from quantile regression fitstat_quant_line
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 ituse_label
Convert two numeric ternary outcomes into a factorxy_outcomes2factor xy_thresholds2factor