ggpmisc v0.3.0

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Miscellaneous Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Specialization of method ggplot(): accept and convert on the fly time series data. Geom: "table", adds tables to plots. Statistics: locate and tag peaks and valleys in 2D plots; count observations in different quadrants of a plot; select observations based on 2D density; label with the equation of a polynomial fitted with lm() 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' are supported.

Readme

ggpmisc

cran
version cran
checks

Package ‘ggpmisc’ (Miscellaneous Extensions to ‘ggplot2’) is a set of extensions to R package ‘ggplot2’ (>= 3.0.0) with emphasis on annotations and highlighting related to fitted models and data summaries. To complement these, the widely useful geom_table() and stat_fmt_tb() are defined as well as ggplot constructors for time series objects. The provided ggplot.ts() and ggplot.xts() use try_tibble() which is also exported and accepts objects of additional classes as input.

Statistics useful for highlighting and/or annotating individual data points in regions of plot panels with high/low densities of observations. These stats are designed to work well together with geom_text_repel() and geom_label_repel() from package ‘ggrepel’.

Note: Functions for the manipulation of layers in ggplot objects and statistics and geometries that echo their data input to the R console, earlier included in this package are now in package ‘gginnards’.

Examples

library(ggplot2)
library(ggpmisc)

In the first example we plot a time series using the specialized version of ggplot() that converts the time series into a tibble and maps the x and y aesthetics automatically. We also highlight and label the peaks using stat_peaks.

ggplot(lynx, as.numeric = FALSE) + geom_line() + 
  stat_peaks(colour = "red") +
  stat_peaks(geom = "text", colour = "red", angle = 66,
             hjust = -0.1, x.label.fmt = "%Y") +
  expand_limits(y = 8000)

In the second example we add the equation for a fitted polynomial plus the adjusted coefficient of determination to a plot showing the observations plus the fitted curve and confidence band. We use stat_poly_eq().

formula <- y ~ x + I(x^2)
ggplot(cars, aes(speed, dist)) +
  geom_point() +
  geom_smooth(method = "lm", formula = formula) +
  stat_poly_eq(aes(label =  paste(..eq.label.., ..adj.rr.label.., sep = "~~~~")),
               formula = formula, parse = TRUE)

The same figure as in the second example but this time annotated with the ANOVA table for the model fit. We use stat_fit_tb() which can be used to add ANOVA or summary tables.

formula <- y ~ x + I(x^2)
ggplot(cars, aes(speed, dist)) +
  geom_point() +
  geom_smooth(method = "lm", formula = formula) +
  stat_fit_tb(method = "lm",
              method.args = list(formula = formula),
              tb.type = "fit.anova",
              tb.vars = c(Effect = "term", 
                          "df",
                          "M.S." = "meansq", 
                          "italic(F)" = "statistic", 
                          "italic(P)" = "p.value"),
               label.y.npc = "top", label.x.npc = "left",
              parse = TRUE)
#> Warning in seq.default(along = x): partial argument match of 'along' to
#> 'along.with'

Installation

Installation of the most recent stable version from CRAN:

install.packages("ggspectra")

Installation of the current unstable version from Bitbucket:

# install.packages("devtools")
devtools::install_bitbucket("aphalo/ggspectra")

Documentation

HTML documentation is available at (http://docs.r4photobiology.info/ggpmisc/), including a User Guide.

News on updates to the different packages of the ‘r4photobiology’ suite are regularly posted at (https://www.r4photobiology.info/).

Contributing

Please report bugs and request new features at (https://bitbucket.org/aphalo/ggpmisc/issues). Pull requests are welcome at (https://bitbucket.org/aphalo/ggpmisc).

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Citation

If you use this package to produce scientific or commercial publications, please cite according to:

citation("ggpmisc")
#> 
#> To cite ggpmisc in publications, please use:
#> 
#>   Pedro J. Aphalo. (2016) Learn R ...as you learnt your mother
#>   tongue. Leanpub, Helsinki.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Book{,
#>     author = {Pedro J. Aphalo},
#>     title = {Learn R ...as you learnt your mother tongue},
#>     publisher = {Leanpub},
#>     year = {2016},
#>     url = {https://leanpub.com/learnr},
#>   }

License

© 2016-2018 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.

Functions in ggpmisc

Name Description
stat_fit_tb Model-fit summary or ANOVA
try_data_frame Convert an R object into a tibble
ggplot Create a new ggplot plot from time series data
stat_fit_augment Augment data with fitted values and statistics
stat_dens2d_labels Reset labels of observations in high density regions
stat_dens2d_filter Filter observations by local density
geom_table Tables
find_peaks Find local maxima or global maximum (peaks)
gtb_draw_panel_fun Stat* Objects
stat_quadrat_counts Renamed to stat_quadrant_counts
ggpmisc-package ggpmisc: Miscellaneous Extensions to 'ggplot2'
Moved Moved to package 'gginnards'
stat_peaks Local maxima (peaks) or minima (valleys)
stat_quadrant_counts Number of observations in quadrants
stat_fit_glance One row summary data frame for a fitted model
stat_fit_deviations Residuals from model fit as segments
stat_fit_tidy One row data frame with fitted parameter estimates
stat_poly_eq Equation, p-value, R^2, AIC or BIC of fitted polynomial
stat_fit_residuals Residuals from a model fit
stat_fmt_tb Select and slice a tibble nested in data
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Vignettes of ggpmisc

Name
user-guide.Rmd
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Details

Type Package
Date 2018-07-16
License GPL (>= 2)
LazyData TRUE
LazyLoad TRUE
ByteCompile TRUE
URL https://www.r4photobiology.info, https://bitbucket.org/aphalo/ggpmisc
BugReports https://bitbucket.org/aphalo/ggpmisc/issues
RoxygenNote 6.0.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2018-07-16 11:12:08 UTC; aphalo
Repository CRAN
Date/Publication 2018-07-16 13:40:03 UTC

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