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plot.describe <- function(x, which=c('both', 'continuous', 'categorical'),
what=NULL, sort=c('ascending', 'descending', 'none'),
n.unique=10, digits=5, bvspace=2, ...) {
which <- match.arg(which)
pty <- grType() == 'plotly' && requireNamespace("plotly")
auto <- .Options$plotlyauto
auto <- length(auto) && auto
if(length(what)) x <- x[what]
sort <- match.arg(sort)
specs <- if(pty) markupSpecs$html else markupSpecs$plain
if(bvspace == 1) stop('bvspace may not be 1.0')
format_counts <- function(s) {
bl <- ' '
na <- substring(paste(names(s), bl, sep=''), 1,
max(nchar(names(s))))
va <- paste(substring(bl, 1,
max(nchar(s)) - nchar(s) + 1), s, sep='')
zz <- paste(na, va, sep=':')
gsub(' ', specs$space, zz)
}
fmtlab <- function(x) {
lab <- sub('^.*:', '', x$descript)
if(length(x$units)) lab <- specs$varlabel(lab, x$units)
lab
}
ge <- function(i) unlist(lapply(w, function(x) x[[i]]))
if(which != 'continuous') {
f <- function(x) {
s <- x$counts
v <- x$values
type <- if('Sum' %in% names(s)) 'binary'
else
if(length(v) && is.list(v) &&
all(names(v) == c('value', 'frequency')) &&
is.character(v$value) && length(v$value) <= 20) 'categorical'
else 'none'
if(type == 'none')
return(data.frame(prop=numeric(0), text=character(0)))
n <- as.numeric(s['n'])
if(type == 'binary') {
val <- ''
freq <- as.numeric(s['Sum'])
}
else {
val <- v$value
freq <- v$frequency
}
category <- if(type == 'categorical') val else ''
text <-
paste(category, if(type == 'categorical') ' ',
round(freq / n, 3), specs$frac(freq, n, size=90))
## Details about variable for minimum frequency category
left <- which.min(freq)[1]
text[left] <- paste(c(fmtlab(x), text[left], format_counts(s)),
collapse=specs$br)
y <- if(type == 'binary') 0 else 1 : length(freq)
y <- c(bvspace, rep(1, length(freq) - 1))
## extra 1 for between-variable spacing
j <- switch(sort,
ascending = order(freq),
descending= order(-freq),
none = TRUE)
data.frame(prop=freq[j] / n, y=y, text=I(text[j]),
category=I(category[j]),
missing=as.numeric(s['missing']), nlev=length(freq))
}
w <- lapply(x, f)
nam <- names(w)
for(na in nam) {
l <- length(w[[na]]$prop)
w[[na]]$xname <- if(l) rep(na, l) else character(0)
}
if(length(ge('xname')) == 0) {
warning('no categorical variables found')
pcat <- NULL
} else {
z <- data.frame(xname = I(ge('xname')),
Proportion = ge('prop'),
y = ge('y'),
text = I(ge('text')),
category = I(ge('category')),
Missing = ge('missing'),
nlev = ge('nlev'))
un <- unique(z$xname)
nv <- length(un)
z$xnamef <- factor(z$xname, levels=un)
z$xnamen <- as.integer(z$xnamef) - z$y / pmax(0.7 * nv, z$nlev)
z$cumy <- cumsum(z$y)
if(! pty) z$cumy <- - z$cumy
tly <- z$cumy[z$y == bvspace]
if(! pty) {
r <- range(z$Proportion)
z$proplev <- r[2] + .2
pcat <-
if(any(z$Missing > 0))
ggplot(z, aes(text=text)) +
geom_point(aes(x=Proportion, y=cumy, color=Missing)) +
geom_text(aes(x=proplev, y=cumy, label=category),
size=2.5, hjust=1) +
scale_y_continuous(breaks=tly, labels=un) +
scale_x_continuous(breaks=pretty(r)) +
scale_color_gradientn(colors=viridisLite::viridis(10)) +
ylab(NULL) +
theme(panel.grid.minor.y = element_blank())
else
ggplot(z, aes(text=text)) + geom_point(aes(x=Proportion, y=cumy)) +
geom_text(aes(x=proplev, y=cumy, label=category),
size=2.5, hjust=1) +
scale_y_continuous(breaks=tly, labels=un) +
scale_x_continuous(breaks=pretty(r)) +
ylab(NULL) +
theme(panel.grid.minor.y = element_blank())
}
else
{
z$proplev <- 1.15
pcat <- if(any(z$Missing > 0))
plotly::plot_ly(z, x = ~ Proportion, y= ~ cumy, text= ~ text,
color=~ Missing, mode='markers',
hoverinfo='text',
type='scatter', name='',
height=if(! auto) plotlyParm$heightDotchart(nrow(z)))
else
plotly::plot_ly(z, x=~ Proportion, y=~ cumy, text=~ text,
mode='markers', hoverinfo='text',
type='scatter', name='',
height=if(! auto) plotlyParm$heightDotchart(nrow(z)))
pcat <-
plotly::add_trace(pcat,
data=z, x=~ proplev, y=~ cumy, text=~ category,
mode='text', textposition='left',
textfont=list(size=9), hoverinfo='none',
name='Levels')
tl <- seq(0, 1, by=0.05)
## X tick mark labels for multiples of 0.1
tt <- ifelse(tl %% 0.1 == 0, as.character(tl), '')
tly <- z$cumy[z$y == bvspace]
pcat <- plotly::layout(pcat,
xaxis=list(range=c(0,1.15), zeroline=TRUE,
tickvals=tl, ticktext=tt,
title='Proportion'),
yaxis=list(title='', autorange='reversed',
tickvals=tly, ticktext=un),
margin=list(l=plotlyParm$lrmargin(un)))
}
}
}
if(which != 'categorical') {
f <- function(x) {
s <- x$counts
v <- x$values
isn <- function(z) is.numeric(z) || testDateTime(z, 'either')
if(! (as.numeric(s['distinct']) >= n.unique &&
length(v) && is.list(v) &&
all(names(v) == c('value', 'frequency')) &&
isn(v$value)) )
return(data.frame(X=numeric(0), count=numeric(0), text=character(0)))
X <- v$value
Y <- v$frequency
Xn <- as.numeric(X)
text <- paste(format(X, digits=digits), ' (n=', Y, ')', sep='')
X <- (Xn - Xn[1]) / diff(range(Xn))
zz <- format_counts(s)
lab <- fmtlab(x)
text[1] <- paste(c(lab, text[1], zz), collapse='<br>')
## Note: plotly does not allow html tables as hover text
m <- rep(as.numeric(s['missing']), length(X))
list(X=X, prop=Y / sum(Y), text=I(text), missing=m)
}
w <- lapply(x, f)
nam <- names(w)
for(n in nam) {
l <- length(w[[n]]$X)
w[[n]]$xname <- if(l) rep(n, l) else character(0)
}
if(length(ge('xname')) == 0) {
warning('no continuous variables found')
pcon <- NULL
} else {
z <- data.frame(xname = I(ge('xname')),
X = ge('X'),
Proportion = round(ge('prop'), 4),
text = I(ge('text')),
Missing = ge('missing'))
z <- z[nrow(z) : 1, ] # so plotly will keep right ordering
unam <- unique(z$xname)
z$yy <- match(as.character(z$xname), unam)
## Scale Proportion so that max over all variables is 0.9
z$Proportion <- 0.9 * z$Proportion / max(z$Proportion)
g <- if(any(z$Missing > 0))
ggplot(z, aes(text=text)) +
geom_segment(aes(x=X, xend=X, y=yy, yend=yy + Proportion,
color=Missing)) +
scale_y_continuous(breaks=1 : length(unam), labels=unam) +
scale_color_gradientn(colors=viridisLite::viridis(10)) +
xlab(NULL) + ylab(NULL) +
theme(axis.text.x = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
panel.grid.minor.y = element_blank(),
axis.ticks.x = element_blank())
else
ggplot(z, aes(text=text)) +
geom_segment(aes(x=X, xend=X, y=yy, yend=yy + Proportion)) +
scale_y_continuous(breaks=1 : length(unam), labels=unam) +
xlab(NULL) + ylab(NULL) +
theme(axis.text.x = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
panel.grid.minor.y = element_blank(),
axis.ticks.x = element_blank())
## ggplotly would not hover text at x=0 when height < 350 px
curtail <- function(x) min(1000, max(x, 350))
pcon <- if(! pty) g
else
plotly::ggplotly(g, tooltip='text', width=if(! auto) 800,
height=if(! auto) curtail(60 + 25 * length(unam)))
## If don't run plot_ly, hovering will pop up all vertical points
# pcon <- if(any(z$missing > 0))
# plotly::plot_ly(z, x=X, y=yy, mode='markers',
# color=missing, colors=colors, name='')
# else
# plotly::plot_ly(z, x=X, y=yy, mode='none', name='')
#
# pcon <- with(z, histSpikep(NULL, x=X, y=yy, z=Proportion,
# hovertext=text, tracename='',
# color=if(any(missing > 0)) missing,
# colors=colors))
## Note: plotly does not allow font, color, size changes for hover text
# pcon <- if(any(z$missing > 0))
# plotly::plot_ly(z, x=X, y=xname, size=Proportion, text=text,
# color=missing, mode='markers',
# marker=list(symbol='line-ns-open'),
# type='scatter', hoverinfo='text')
# else
# plotly::plot_ly(z, x=X, y=xname, size=Proportion,
# text=text,
# mode='markers',
# marker=list(symbol='line-ns-open'),
# type='scatter', hoverinfo='text')
#
# maxlen <- max(nchar(as.character(unam)))
# pcon <- plotly::layout(pcon, xaxis=list(title='', showticklabels=FALSE,
# zeroline=FALSE, showgrid=FALSE),
# yaxis=list(title='',
# tickvals=1 : length(unam),
# ticktext=unam),
# margin=list(l=max(70, maxlen * 6)),
# autosize=TRUE, evaluate=TRUE)
}
}
if(which == 'both') {
if(! length(pcat)) return(pcon)
if(! length(pcon)) return(pcat)
}
## knitr.in.progress not set to TRUE unless explicitly select menu
## choice knit to html. Even when properly set, resulting html
## file was messed up as plotly widgets were duplicated
switch(which,
categorical = pcat,
continuous = pcon,
both = if(FALSE && pty &&
isTRUE(getOption('knitr.in.progress')))
htmltools::tagList(list(plotly::as.widget(pcat),
plotly::as.widget(pcon)))
else
list(Categorical=pcat, Continuous=pcon))
}
## Some of these are for dotchart3.s
utils::globalVariables(c('X', 'Proportion', 'xname', 'cumy', 'proplev',
'category', 'xb', 'Missing', 'yy'))
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