showSignificance: Annotate significance of results on plots

In dcousin3/superb: Summary Plots with Adjusted Error Bars

Annotate significance of results on plots

Description

showSignificance is used to add an annotation to a ggplot in the form of a bracket with a text. The bracket extends from x range (left, right) with a heigth of width. It is also possible to have the bracket and the text vertical when y is a range (bottom, top).

Usage

showSignificance(
  x,
  y,
  width,
  text = NULL,
  panel = list(),
  segmentParams = list(),
  textParams = list()
)

Arguments

x	(a vector of 2 when horizontal) indicates the limits of the annotation;
y	(a vector of 2 when vertical) the location of the annotation in the y direction
width	height of the annotation; for negative width, the legs extends towards the bottom;
text	(optional) string text to be display on the opposite side of width;
panel	(optional) a list to identify in which panel to put the annotation;
segmentParams	(optional) a list of directives that will be sent to the geom_segment items;
textParams	(optional) a list of directives that will be sent to the geom_text item.

Value

adds an annotation in a ggplot

Examples

# loading required libraries
library(superb)
library(ggplot2)
library(grid)

# making one random data set with three factors 2 x 3 x (3)
dta <- GRD(
    SubjectsPerGroup = 20,
    BSFactors = c("Group(2)","Age(3)"), 
    WSFactors = c("Moment(3)"),
    Population = list(mean = 75, stddev = 5),
    Effects   = list("Group" = slope(10) )
)

# making a two-factor plot and a three-factor plots (having panels)
plt2 <- superb(
        cbind(DV.1,DV.2,DV.3) ~ Group, 
        dta, 
        WSFactor = c("Moment(3)"),
        adjustments = list(purpose="difference"),
        factorOrder = c("Moment","Group")
    )
plt3 <- superb(
        cbind(DV.1,DV.2,DV.3) ~ Group + Age, 
        dta,
        WSFactor = c("Moment(3)"),
        adjustments = list(purpose="difference"),
        factorOrder = c("Moment","Group","Age")
    )

# lets decorate these plots a bit...
plt2 <- plt2 +  scale_fill_manual( name = "Group", 
        labels = c("Easy", "Hard"), 
        values = c("blue", "purple")) + 
  scale_colour_manual( name = "Group", 
        labels = c("Easy", "Hard"), 
        values = c("blue", "purple")) +
  coord_cartesian( ylim = c(50,100), xlim = c(0.5, 3.9) )
plt3 <- plt3 +  scale_fill_manual( name = "Group", 
        labels = c("Easy", "Hard"), 
        values = c("blue", "purple")) + 
  scale_colour_manual( name = "Group", 
        labels = c("Easy", "Hard"), 
        values = c("blue", "purple")) +
  coord_cartesian( ylim = c(50,105) )

# a very basic example
plt2 +  showSignificance( c(0.75, 1.25), 90, -1, "++1++")

# the annotation can be vertical when y is a vector with bottom and top location:
plt2 + showSignificance( 3.75, c(70,80), -0.1, "++1++")

# an example with panels; the "panel" argument is used to identify on 
# which panel to put the annotation (or else they appear on all panels)
# and with arms of differing lengths, and one flat ending
plt3 + 
    showSignificance( c(0.75, 1.25), 90, -2.5,      "++1++", panel = list(Age= 1)) + 
    showSignificance( c(1.75, 2.25), 90, -2.5,      "++2++", panel = list(Age= 2)) + 
    showSignificance( c(0.75, 1.25), 90, c(-10,-5), "++3++", panel = list(Age= 3)) +
    showSignificance( c(2.00, 3.25), 95, -10,       "++4++", panel = list(Age= 3)) + 
    showSignificance( c(1.75, 2.25), 85, 0,                  panel = list(Age= 3))  

# here, we send additional directives to the annotations
plt3 + 
    showSignificance( c(0.75, 1.25), 90, -5,  "++1++", panel = list(Age= 1)) + 
    showSignificance( c(1.75, 2.25), 95, -10, "++2++", panel = list(Age = 2),
        textParams    = list(size = 3,              # smaller font
                            family  = "mono",       # courrier font
                            colour= "chartreuse3"   # dark green color
        ), 
        segmentParams = list(linewidth = 1.,             # thicker lines
                            arrow   = arrow(length = unit(0.2, "cm") ), # arrow heads
                            colour = "chartreuse3"  # dark green color as well
        )
    ) +
    showSignificance( c(1.75, 3.25), 95, -30, "++3++", panel = list(Age = 3),
        textParams    = list(size = 5,              # larger font
                            family  = "serif",      # times font
                            alpha = 0.3 ),          # transparent
        segmentParams = list(linewidth = 2., 
                            arrow   = arrow(length = unit(0.2, "cm") ), 
                            alpha = 0.3, 
                            lineend = "round"       # so that line end overlap nicely
        )
    )

dcousin3/superb documentation built on Oct. 29, 2024, 5:28 p.m.