Plot an emmGrid or summary_emm object — plot.emmGrid • emmeans

Methods are provided to plot EMMs as side-by-side CIs, and optionally to display “comparison arrows” for displaying pairwise comparisons.

Usage

# S3 method for class 'emmGrid'
plot(x, y, type, CIs = TRUE, PIs = FALSE,
  comparisons = FALSE, colors, alpha = 0.05, adjust = "tukey",
  int.adjust = "none", intervals, ...)

# S3 method for class 'summary_emm'
plot(x, y, horizontal = TRUE, CIs = TRUE, xlab, ylab,
  layout, scale = NULL, colors, intervals, plotit = TRUE, ...)

Arguments

x: Object of class emmGrid or summary_emm
y: (Required but ignored)
type: Character value specifying the type of prediction desired (matching "linear.predictor", "link", or "response"). See details under summary.emmGrid. In addition, the user may specify type = "scale", in which case a transformed scale (e.g., a log scale) is displayed based on the transformation or link function used. Additional customization of this scale is available through including arguments to ggplot2::scale_x_continuous in ... .
CIs: Logical value. If TRUE, confidence intervals are plotted for each estimate.
PIs: Logical value. If TRUE, prediction intervals are plotted for each estimate. If object is a Bayesian model, this requires the ... arguments to include frequentist = TRUE and sigma = (some value). Note that the PIs option is not available with summary_emm objects – only for emmGrid objects. Also, prediction intervals are not available with engine = "lattice".
comparisons: Logical value. If TRUE, “comparison arrows” are added to the plot, in such a way that the degree to which arrows overlap reflects as much as possible the significance of the comparison of the two estimates. (A warning is issued if this can't be done.) Note that comparison arrows are not available with `summary_emm` objects.
colors: Optional character vector of colors to use for estimates, CIs, PIs, and comparison arrows, respectively. If missing, these are derived from ink, paper, and accent in the theme's geom element. ink is used for the estimates, accent is used for comparison arrows, and a contrasting color to accent is blended with paper for the intervals. If just one color is given, estimates and intervals are made from various blends of that color and paper, and accent color is used for comparison arrows.
alpha: The significance level to use in constructing comparison arrows
adjust: Character value: Multiplicity adjustment method for comparison arrows only.
int.adjust: Character value: Multiplicity adjustment method for the plotted confidence intervals only.
intervals: If specified, it is used to set CIs. This is the previous argument name for CIs and is provided for backward compatibility.
...: Additional arguments passed to update.emmGrid, summary.emmGrid, predict.emmGrid, or dotplot
horizontal: Logical value specifying whether the intervals should be plotted horizontally or vertically
xlab: Character label for horizontal axis
ylab: Character label for vertical axis
layout: Numeric value passed to dotplot when engine == "lattice".
scale: Object of class trans (in the scales package) to specify a nonlinear scale. This is used in lieu of type = "scale" when plotting a summary_emm object created with type = "response". This is ignored with other types of summaries.
plotit: Logical value. If TRUE, a graphical object is returned; if FALSE, a data.frame is returned containing all the values used to construct the plot.

Value

If plotit = TRUE, a graphical object is returned.

If plotit = FALSE, a data.frame with the table of EMMs that would be plotted. In the latter case, the estimate being plotted is named the.emmean, and any factors involved have the same names as in the object. Confidence limits are named lower.CL and upper.CL, prediction limits are named lpl and upl, and comparison-arrow limits are named lcmpl and ucmpl. There is also a variable named pri.fac which contains the factor combinations that are not among the by variables.

Note

In order to play nice with the plotting functions, any variable names that are not syntactically correct (e.g., contain spaces) are altered using make.names.

Details

If any by variables are in force, the plot is divided into separate panels. For "summary_emm" objects, the ... arguments in plot are passed only to dotplot, whereas for "emmGrid" objects, the object is updated using ... before summarizing and plotting.

In plots with comparisons = TRUE, the resulting arrows are only approximate, and in some cases may fail to accurately reflect the pairwise comparisons of the estimates – especially when estimates having large and small standard errors are intermingled in just the wrong way. Note that the maximum and minimum estimates have arrows only in one direction, since there is no need to compare them with anything higher or lower, respectively. See the vignette("xplanations", "emmeans") for details on how these are derived.

If adjust or int.adjust are not supplied, they default to the internal adjust setting saved in pairs(x) and x respectively (see update.emmGrid).

Examples

warp.lm <- lm(breaks ~ wool * tension, data = warpbreaks)
warp.emm <- emmeans(warp.lm, ~ tension | wool)
plot(warp.emm)


plot(warp.emm, PIs = TRUE, comparisons = TRUE)


with_emm_options(gg.theme = ggplot2::theme_dark(), 
    plot(warp.emm, PIs = TRUE, comparisons = TRUE))


plot(warp.emm, by = NULL, comparisons = TRUE, adjust = "none", 
     horizontal = FALSE, colors = "blue")


### Using a transformed scale
pigs.lm <- lm(log(conc + 2) ~ source * factor(percent), data = pigs)
pigs.emm <- emmeans(pigs.lm, ~ percent | source)
plot(pigs.emm, type = "scale", breaks = seq(20, 100, by = 10))


# Based on a summary. 
# To get a transformed axis, must specify 'scale'; but it does not necessarily
# have to be the same as the actual response transformation
pigs.ci <- confint(pigs.emm, type = "response")
plot(pigs.ci, scale = scales::log10_trans())