DurgaPlot with confidence bracketsBrackets are added to a DurgaPlot that already exists. That means you
must ensure there is sufficient space for the brackets above the plot. To do
this, either specify ylim to DurgaPlot, or create a
large top margin (par(mar = c(...))) and the turn off the plot frame
(DurgaPlot(..., frame.plot = FALSE)). In either case, experiment with
the values until the result is visually pleasing. The annotation can be drawn
into the margin as it will not be cropped.
DurgaBrackets(
plot.stats,
contrasts,
labels = "level CI",
br.lwd = NULL,
br.col = NULL,
br.lty = 1,
lb.col = NULL,
lb.font = NULL,
lb.cex = 1,
snap.to = 1,
shorten = 1.5,
tip.length = 2,
data.gap = 2.5,
vertical.gap = 1.3,
text.pad = 1.5,
round.fn = function(x) signif(x, 2),
...
)No return value. DurgaBrackets is called for its side effect
of adding confidence brackets to the current plot.
Object returned by the call to DurgaPlot
Set of contrasts (i.e. group comparisons) to be displayed as
brackets. Defaults to contrasts passed to DurgaDiff. Can be
specified as a character string ("group 1 - group 2") or a list of
DurgaDiff objects. The bracket label always displays the effect size
for right-hand-group - left-hand-group, regardless of the order that groups
are specified in contrasts, i.e. contrasts = "G1 - G2" will
appear the same as contrasts = "G2 - G1".
Text to display above each bracket. May be NULL, otherwise one
of: "diff" (displayed text is "<difference in means>"),
"CI" ("[<lower>, <upper>]"), "level CI" ("<level>% CI [<lower>,
<upper>]") or "diff CI" ("<difference in means> [<lower>,
<upper>]"); a vector of texts to display for each element of diffs,
or a function called with one argument; a DurgaGroupDiff object,
which should return the label to be displayed.
Graphical parameters (colour, line weight and
style) that control the bracket appearance - passed to
segments. May be a single value or a vector with
one value per bracket. Refer to Details for default values.
Graphical parameters (colour, scale and font)
that control the label appearance - passed to text.
May be a single value or a vector with one value per bracket. Refer to
Details for default values.
Snaps the base of the lowest brackets onto horizontal grid
lines separated by snap.to mm. Used to improve aesthetics of
vertical alignment.
Amount (mm) to shrink brackets at each end
Length of bracket tips (mm). May be a vector with length 2; length of tip at groups 1 and 2 respectively
Vertical distance (mm) between top-most data point and bottom of bracket
Vertical distance (mm) between overlapping brackets
Gap (mm) between bracket and text
By default, numbers displayed as text are printed to 2
significant figures. To change this behaviour, set round.fn to a
function with one argument that converts its argument to the value to be
displayed.
Additional arguments passed to text
Default values for br.lwd, br.col, lb.col and
lb.font depend on the confidence intervals (CI) being plotted. If the
CI covers 0, brackets and text are grey. If the CI does not cover 0, text is
dark grey and bold, and brackets are dark grey with a line width of 2.
DurgaPlot
d <- DurgaDiff(petunia, 1, 2)
# Don't draw frame because brackets will appear in the upper margin
p <- DurgaPlot(d, ef.size = FALSE, frame.plot = FALSE)
# Add the brackets to the plot
DurgaBrackets(p, lb.cex = 0.8)
# Only draw brackets that do not include zero
p <- DurgaPlot(d, ef.size = FALSE, frame.plot = FALSE)
diffs <- Filter(function(pwes) (pwes$bca[4] > 0 || pwes$bca[5] < 0), p$es$group.differences)
DurgaBrackets(p, contrasts = diffs)
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