##################################################################
##################################################################
## Three moderately-advanced plot layout: pointjitter,
## pointlinejitter, pointjitterviolin, pointindividualline
##################################################################
##################################################################
######################################################################################
#' @name superbPlot.pointjitter
#'
#' @title superbPlot point-and-jitter dots layout
#'
#' @md
#'
#' @description superbPlot comes with a few built-in templates for making the final plots.
#' All produces ggplot objects that can be further customized. Additionally, it is
#' possible to add custom-make templates (see vignette 6). The functions, to be
#' "superbPlot-compatible", must have these parameters:
#'
#' @param summarydata a data.frame with columns "center", "lowerwidth" and "upperwidth" for each level of the factors;
#' @param xfactor a string with the name of the column where the factor going on the horizontal axis is given;
#' @param groupingfactor a string with the name of the column for which the data will be grouped on the plot;
#' @param addfactors a string with up to two additional factors to make the rows and columns panels, in the form "fact1 ~ fact2";
#' @param rawdata always contains "DV" for each participants and each level of the factors
#' @param pointParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param jitterParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param errorbarParams (optional) list of graphic directives that are sent to the geom_superberrorbar layer
#' @param facetParams (optional) list of graphic directives that are sent to the facet_grid layer
#' @param xAsFactor (optional) Boolean to indicate if the factor on the horizontal should continuous or discrete (default is discrete)
#'
#' @return a ggplot object
#'
#' @examples
#' # This will make a plot with jittered points, aka dot plots
#' superb(
#' len ~ dose + supp,
#' ToothGrowth,
#' plotStyle="pointjitter"
#' )
#'
#' # if you extract the data with superbData, you can
#' # run this layout directly
#' #processedData <- superb(
#' # len ~ dose + supp,
#' # ToothGrowth,
#' # showPlot = FALSE
#' #)
#' #
#' #superbPlot.pointjitter(processedData$summaryStatistic,
#' # "dose",
#' # "supp",
#' # ".~.",
#' # processedData$rawData)
#'
#' @export superbPlot.pointjitter
#'
######################################################################################
superbPlot.pointjitter <- function(
summarydata, # a summary result data.frame
xfactor, # the factor on the horizontal axis
groupingfactor, # the factor for multiple lines/bars within the plot
addfactors, # the factor(s) to make multiple panels
rawdata, # the raw data in long format
# what follows are optional
pointParams = list(),
jitterParams = list(),
errorbarParams = list(),
facetParams = list(),
xAsFactor = TRUE # should the horizontal axis be continuous?
) {
runDebug("pointjitter", "Entering superbPlot.pointjitter",
c("xfactor2", "groupingfactor2", "addfactors2","pointParams2","jitterParams2","errorbarParams2"), list(xfactor, groupingfactor, addfactors, pointParams, jitterParams, errorbarParams))
mysym <- function(x) { if(is.character(x)) sym(x) else x }
# rename column "DV" to "center"
rawdata$center <- rawdata$DV
# depending on the scale of the x-axis.
if (!xAsFactor) {
summarydata[[xfactor]] = unfactor(summarydata[[xfactor]])
rawdata[[xfactor]] = unfactor(rawdata[[xfactor]])
}
# determining the type of jitter based on the presence or not of a groupingfac
if (is.null(groupingfactor)) {
do_jitters = do.call(geom_jitter, modifyList(
list(data = rawdata, alpha = 0.2, width = 0.2, height = 0.0,
mapping = aes(y = center ) ),
jitterParams
) )
} else {
do_jitters = do.call(geom_point, modifyList(
list(data = rawdata , alpha = 0.2,
position = position_jitterdodge(jitter.width=0.1 , dodge.width=0.5 ),
mapping = aes(y = center, color = !!mysym(groupingfactor) ) ),
jitterParams
) )
}
# let's do the plot!
plot <- ggplot(
summarydata,
aes( x = !!mysym(xfactor), color = !!mysym(groupingfactor) )
) +
# the jitters
do_jitters +
# the points
do.call(geom_point, modifyList(
list(position = position_dodge(width = .5),
size=3,
mapping = aes(group = !!mysym(groupingfactor), y = center ) ),
pointParams
)) +
# the error bars; define ymin, ymax only in errorbar
do.call(geom_superberrorbar, modifyList(
list(position = position_dodge(.5), width = 0.1, linewidth = 0.75,
mapping = aes(group = !!mysym(groupingfactor), ymin = center + lowerwidth, ymax = center + upperwidth) ),
errorbarParams
)) +
# the panels (rows or both rows and columns, NULL if no facet)
do.call( facet_grid, modifyList(
list( rows = addfactors ),
facetParams
))
return(plot)
}
######################################################################################
#' @name superbPlot.pointlinejitter
#'
#' @title superbPlot point-and-jitter lines layout
#'
#' @md
#'
#' @description superbPlot comes with a few built-in templates for making the final plots.
#' All produces ggplot objects that can be further customized. Additionally, it is
#' possible to add custom-make templates (see vignette 6). The functions, to be
#' "superbPlot-compatible", must have these parameters:
#'
#' @param summarydata a data.frame with columns "center", "lowerwidth" and "upperwidth" for each level of the factors;
#' @param xfactor a string with the name of the column where the factor going on the horizontal axis is given;
#' @param groupingfactor a string with the name of the column for which the data will be grouped on the plot;
#' @param addfactors a string with up to two additional factors to make the rows and columns panels, in the form "fact1 ~ fact2";
#' @param rawdata always contains "DV" for each participants and each level of the factors
#' @param pointParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param lineParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param jitterParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param errorbarParams (optional) list of graphic directives that are sent to the geom_superberrorbar layer
#' @param facetParams (optional) list of graphic directives that are sent to the facet_grid layer
#' @param xAsFactor (optional) Boolean to indicate if the factor on the horizontal should continuous or discrete (default is discrete)
#'
#' @return a ggplot object
#'
#' @examples
#' # This will make a plot with jittered points, aka dot plots
#' superb(
#' len ~ dose + supp,
#' ToothGrowth,
#' plotStyle="pointlinejitter"
#' )
#'
#' # if you extract the data with superbData, you can
#' # run this layout directly
#' #processedData <- superb(
#' # len ~ dose + supp,
#' # ToothGrowth,
#' # showPlot = FALSE
#' #)
#' #
#' #superbPlot.pointlinejitter(processedData$summaryStatistic,
#' # "dose",
#' # "supp",
#' # ".~.",
#' # processedData$rawData)
#'
#' @export superbPlot.pointlinejitter
#'
######################################################################################
superbPlot.pointlinejitter <- function(
summarydata, # a summary result data.frame
xfactor, # the factor on the horizontal axis
groupingfactor, # the factor for multiple lines/bars within the plot
addfactors, # the factor(s) to make multiple panels
rawdata, # the raw data in long format
# what follows are optional
pointParams = list(),
lineParams = list(),
jitterParams = list(),
errorbarParams = list(),
facetParams = list(),
xAsFactor = TRUE # should the horizontal axis be continuous?
) {
runDebug("pointlinejitter", "Entering superbPlot.pointlinejitter",
c("xfactor2", "groupingfactor2", "addfactors2","pointParams2","jitterParams2","errorbarParams2"), list(xfactor, groupingfactor, addfactors, pointParams, jitterParams, errorbarParams))
mysym <- function(x) { if(is.character(x)) sym(x) else x }
# rename column "DV" to "center"
rawdata$center <- rawdata$DV
# depending on the scale of the x-axis.
if (!xAsFactor) {
summarydata[[xfactor]] = unfactor(summarydata[[xfactor]])
rawdata[[xfactor]] = unfactor(rawdata[[xfactor]])
}
# determining the type of jitter based on the presence or not of a groupingfac
if (is.null(groupingfactor)) {
do_jitters = do.call(geom_jitter, modifyList(
list(data = rawdata, alpha = 0.2, width = 0.2, height = 0.0,
mapping = aes(y = center ) ),
jitterParams
) )
do_lines = do.call(geom_line, modifyList(
list(
mapping = aes(y = center, group = !!mysym(ifelse(is.null(groupingfactor),1,groupingfactor)) ) ),
lineParams
) )
} else {
do_jitters = do.call(geom_point, modifyList(
list(data = rawdata , alpha = 0.2,
position = position_jitterdodge(jitter.width=0.1 , dodge.width=0.5 ),
mapping = aes(y = center, color = !!mysym(groupingfactor) ) ),
jitterParams
) )
do_lines = do.call(geom_line, modifyList(
list(position = position_jitterdodge(jitter.width=0.1 , dodge.width=0.5 ),
mapping = aes(y = center, group = !!mysym(ifelse(is.null(groupingfactor),1,groupingfactor)) ) ),
lineParams
) )
}
# let's do the plot!
plot <- ggplot(
summarydata,
aes( x = !!mysym(xfactor), color = !!mysym(groupingfactor) )
) +
# the lines connecting the points
do_lines +
# the jitters
do_jitters +
# and the points
do.call(geom_point, modifyList(
list(position = position_dodge(width = .5),
size=3,
mapping = aes(group = !!mysym(groupingfactor), y = center ) ),
pointParams
)) +
# the error bars; define ymin, ymax only in errorbar
do.call(geom_superberrorbar, modifyList(
list(position = position_dodge(.5), width = 0.1, linewidth = 0.75,
mapping = aes(group = !!mysym(groupingfactor), ymin = center + lowerwidth, ymax = center + upperwidth) ),
errorbarParams
)) +
# the panels (rows or both rows and columns, NULL if no facet)
do.call( facet_grid, modifyList(
list( rows = addfactors ),
facetParams
))
return(plot)
}
######################################################################################
#' @name superbPlot.pointjitterviolin
#'
#' @title superbPlot point, jitter and violin plot layout
#'
#' @md
#'
#' @description superbPlot comes with a few built-in templates for making the final plots.
#' All produces ggplot objects that can be further customized. Additionally, it is
#' possible to add custom-make templates (see vignette 6). The functions, to be
#' "superbPlot-compatible", must have these parameters:
#'
#' @param summarydata a data.frame with columns "center", "lowerwidth" and "upperwidth" for each level of the factors;
#' @param xfactor a string with the name of the column where the factor going on the horizontal axis is given;
#' @param groupingfactor a string with the name of the column for which the data will be grouped on the plot;
#' @param addfactors a string with up to two additional factors to make the rows and columns panels, in the form "fact1 ~ fact2";
#' @param rawdata always contains "DV" for each participants and each level of the factors
#' @param pointParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param jitterParams (optional) list of graphic directives that are sent to the geom_bar layer
#' @param violinParams (optional) list of graphic directives that are sent to the geom_bar layer
#' this modified geom_violin has additional options "direction"/"antagonize" and "push".
#' @param errorbarParams (optional) list of graphic directives that are sent to the geom_superberrorbar layer
#' @param facetParams (optional) list of graphic directives that are sent to the facet_grid layer
#'
#' @return a ggplot object
#'
#' @examples
#' # This will make a plot with jittered points and violins for the overall distribution
#' superb(
#' len ~ dose + supp,
#' ToothGrowth,
#' plotStyle = "pointjitterviolin"
#' )
#'
#' # if you extract the data with superbData, you can
#' # run this layout directly
#' #processedData <- superb(
#' # len ~ dose + supp,
#' # ToothGrowth,
#' # showPlot = FALSE
#' #)
#' #
#' #superbPlot.pointjitterviolin(processedData$summaryStatistic,
#' # "dose",
#' # "supp",
#' # ".~.",
#' # processedData$rawData)
#'
#' @export superbPlot.pointjitterviolin
#'
######################################################################################
superbPlot.pointjitterviolin <- function(
summarydata, # a summary result data.frame
xfactor, # the factor on the horizontal axis
groupingfactor, # the factor for multiple lines/bars within the plot
addfactors, # the factor(s) to make multiple panels
rawdata, # the raw data in long format
# what follows are optional
pointParams = list(),
jitterParams = list(),
violinParams = list(),
errorbarParams = list(),
facetParams = list()
) {
runDebug("pointjitterviolin", "Entering superbPlot.pointjitterviolin",
c("xfactor2", "groupingfactor2", "addfactors2","pointParams2","jitterParams2","violinParams2","errorbarParams2"), list(xfactor, groupingfactor, addfactors, pointParams, jitterParams, violinParams, errorbarParams))
mysym <- function(x) { if(is.character(x)) sym(x) else x }
# rename column "DV" as "center"
rawdata$center <- rawdata$DV
# find ... (for antagonize = TRUE option)
rawdataB <- rawdata
rawdataB$dir <- rep(0, dim(rawdataB)[1])
# remove antagonize option if present
temp <- FALSE
if (exists("antagonize", where = violinParams)){
temp = violinParams$antagonize
violinParams$antagonize = NULL
} else if (exists("direction", where = violinParams)) {
rawdataB$dir <- violinParams$direction
}
# add the "dir" column with alternating violin directions
if (temp) {
# alternate the directions
tt = unique(rawdataB[[xfactor]])
rawdataB$dir <- 2*(as.numeric(rawdataB[[xfactor]]) %/% 2) -1
}
# determining the type of jitter based on the presence or not of a groupingfac
if (is.null(groupingfactor)) {
do_jitters = do.call(geom_jitter, modifyList(
list(data = rawdata, alpha = 0.2, width = 0.2, height = 0.0,
mapping = aes( y = center ) ),
jitterParams
) )
do_violins = do.call( geom_flat_violin, modifyList(
list(data = rawdataB,
mapping = aes( y = center, direction = dir ),
scale = "area", trim = FALSE, alpha = 0.25),
violinParams
) )
} else {
do_jitters = do.call(geom_point, modifyList(
list(data = rawdata , alpha = 0.2,
position = position_jitterdodge(jitter.width=0.1 , dodge.width=.75 ),
mapping = aes(y = center, group = !!mysym(groupingfactor) ) ),
jitterParams
) )
do_violins = do.call( geom_flat_violin, modifyList(
list(data = rawdataB,
position= position_dodge(0.75), #"dodge",
mapping = aes( y = center, fill = !!mysym(groupingfactor), direction = dir ),
scale = "area", trim = FALSE, alpha = 0.25),
violinParams
) )
}
# let's do the plot!
plot <- ggplot(data = summarydata,
#mapping = aes_string(x = xfactor, colour = groupingfactor )
mapping = aes(x = !!mysym(xfactor), colour = !!mysym(groupingfactor) )
) +
# violins in the back
do_violins +
# jitters second
do_jitters +
# and finally the points and the error bars
do.call( geom_point, modifyList(
list(
#mapping = aes_string(group = groupingfactor, y = "center"),
mapping = aes(group = !!mysym(groupingfactor), y = center),
size = 3, position = position_dodge(.75) ),
pointParams) ) +
do.call( geom_superberrorbar, modifyList(
list(
#mapping = aes_string(group = groupingfactor, ymin = "center+lowerwidth", ymax = "center+upperwidth"),
mapping = aes(group = !!mysym(groupingfactor), ymin = center+lowerwidth, ymax = center+upperwidth),
position = position_dodge(.75), width = 0.1, linewidth = .75),
errorbarParams) )+
do.call( facet_grid, modifyList(
list( rows = addfactors ),
facetParams
))
return(plot)
}
######################################################################################
#' @name superbPlot.pointindividualline
#'
#' @title superbPlot point and individual-line layout for within-subject design
#'
#' @md
#'
#' @description superbPlot comes with a few built-in templates for making the final plots.
#' All produces ggplot objects that can be further customized. Additionally, it is
#' possible to add custom-make templates (see vignette 6). The functions, to be
#' "superbPlot-compatible", must have these parameters:
#'
#' @param summarydata a data.frame with columns "center", "lowerwidth" and "upperwidth" for each level of the factors;
#' @param xfactor a string with the name of the column where the factor going on the horizontal axis is given;
#' @param groupingfactor a string with the name of the column for which the data will be grouped on the plot;
#' @param addfactors a string with up to two additional factors to make the rows and columns panels, in the form "fact1 ~ fact2";
#' @param rawdata always contains "DV" for each participants and each level of the factors
#' @param pointParams (optional) list of graphic directives that are sent to the geom_point layer
#' @param datapointParams (optional) list of graphic directives that are sent to the geom_point layer of the individual lines
#' @param lineParams (optional) list of graphic directives that are sent to the geom_bar layer;
#' the parameter colorize=TRUE with use a distinct color for decreasing segments of line
#' @param errorbarParams (optional) list of graphic directives that are sent to the geom_superberrorbar layer
#' @param facetParams (optional) list of graphic directives that are sent to the facet_grid layer
#'
#' @return a ggplot object
#'
#' @examples
#' # This will make a plot with points and individual lines for each subject's scores
#'
#' # we take the Orange built-in data.frame but shorten the names...
#' names(Orange) <- c("Tree","age","circ")
#' # Makes the plot:
#' superb( circ ~ age | Tree,
#' Orange,
#' adjustments = list(purpose = "difference", decorrelation = "none"),
#' plotStyle= "pointindividualline"
#' )
#'
#' # if you extract the data, you can
#' # run this layout directly
#' #processedData <- superb( circ ~ age | Tree,
#' # Orange,
#' # adjustments = list(purpose = "difference", decorrelation = "none"),
#' #)
#' #
#' #superbPlot.pointindividualline(processedData$summaryStatistic,
#' # "age",
#' # NULL,
#' # ".~.",
#' # processedData$rawData)
#'
#' @export superbPlot.pointindividualline
#' @importFrom utils modifyList
#'
######################################################################################
superbPlot.pointindividualline <- function(
summarydata, # a summary result data.frame
xfactor, # the factor on the horizontal axis
groupingfactor, # the factor for multiple lines/bars within the plot
addfactors, # the factor(s) to make multiple panels
rawdata, # the raw data in long format
# what follows are optional
datapointParams = list(),
pointParams = list(),
lineParams = list(),
errorbarParams = list(),
facetParams = list()
) {
runDebug("pointindividualline", "Entering superbPlot.pointindividualline",
c("xfactor2", "groupingfactor2", "addfactors2","pointParams2","lineParams2","errorbarParams2"), list(xfactor, groupingfactor, addfactors, pointParams, lineParams, errorbarParams))
mysym <- function(x) { if(is.character(x)) sym(x) else x }
# rename column "DV" as "center"
rawdata$center <- rawdata$DV
# find which segments are increasing (for colorize=TRUE option)
rawdataB <- rawdata
if (exists("id", where = rawdata)) {
# indicate if data are increasing or decreasing
rawdataB <- rawdata[order(rawdata$id),]
rawdataB$ypost <- c(with(rawdataB, embed(center,2)[,1]),0)
rawdataB$increase <- factor(rawdataB$ypost > rawdataB$center)
} else {
#print("there is no id column")
}
# remove colorize option if present
temp <- FALSE
if (exists("colorize", where = lineParams)){
temp <- lineParams$colorize
lineParams$colorize <- NULL
}
# compute individual lines
if (temp) {
dolines <- do.call(geom_line, modifyList(
list(data = rawdataB,
linewidth=0.2, alpha = 0.25,
mapping = aes( y = center, group = id, color = increase ) ),
lineParams
))
} else {
dolines <- do.call(geom_line, modifyList(
list(data = rawdata,
linewidth=0.2, alpha = 0.25,
mapping = aes( y = center, group = id ) ),
lineParams
))
}
# let's do the plot!
plot <- ggplot(
data = summarydata,
aes(
x = !!mysym(xfactor),
y = center,
colour = !!mysym(groupingfactor)
)) +
# the individual lines
dolines +
# the individual points
do.call(geom_point, modifyList(
list(data = rawdata, alpha = 0.25,
mapping = aes(group = id) ),
datapointParams
)) +
# the error bars; define ymin, ymax only in errorbar
do.call(geom_superberrorbar, modifyList(
list(position = position_dodge(.5), width = 0.1, linewidth = 0.75,
mapping = aes(group = !!mysym(groupingfactor), ymin = center + lowerwidth, ymax = center + upperwidth) ),
errorbarParams
)) +
# the summary statistics
do.call(geom_point, modifyList(
list(position = position_dodge(width = .5),
size=3,
mapping = aes(group = !!mysym(groupingfactor)) ),
pointParams
)) +
# the panels (rows or both rows and columns, NULL if no facet)
do.call( facet_grid, modifyList(
list( rows = addfactors ),
facetParams
))
return(plot)
}
######################################################
######################################################
## end of the built-in templates
######################################################
######################################################
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.