Hmisc: dotchartpl – R documentation

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dotchartpl

Enhanced Version of dotchart Function for plotly

Description

This function produces a plotly interactive graphic and accepts a different format of data input than the other dotchartx functions. It was written to handle a hierarchical data structure including strata that further subdivide the main classes. Strata, indicated by the mult variable, are shown on the same horizontal line, and if the variable big is FALSE will appear slightly below the main line, using smaller symbols, and having some transparency. This is intended to handle output such as that from the summaryP function when there is a superpositioning variable group and a stratification variable mult, especially when the data have been run through the addMarginal function to create mult categories labelled "All" for which the user will specify big=TRUE to indicate non-stratified estimates (stratified only on group) to emphasize.

When viewing graphics that used mult and big, the user can click on the legends for the small points for groups to vanish the finely stratified estimates.

When group is used by mult and big are not, and when the group variable has exactly two distinct values, you can specify refgroup to get the difference between two proportions in addition to the individual proportions. The individual proportions are plotted, but confidence intervals for the difference are shown in hover text and half-width confidence intervals for the difference, centered at the midpoint of the proportions, are shown. These have the property of intersecting the two proportions if and only if there is no significant difference at the 1 - conf.int level.

Specify fun=exp and ifun=log if estimates and confidence limits are on the log scale. Make sure that zeros were prevented in the original calculations. For exponential hazard rates this can be accomplished by replacing event counts of 0 with 0.5.

Usage

dotchartpl(x, major=NULL, minor=NULL, group=NULL, mult=NULL,
           big=NULL, htext=NULL, num=NULL, denom=NULL,
           numlabel='', denomlabel='',
           fun=function(x) x, ifun=function(x) x, op='-',
           lower=NULL, upper=NULL,
           refgroup=NULL, sortdiff=TRUE, conf.int=0.95,
           minkeep=NULL, xlim=NULL, xlab='Proportion',
           tracename=NULL, limitstracename='Limits',
           nonbigtracename='Stratified Estimates',
           dec=3, width=800, height=NULL,
           col=colorspace::rainbow_hcl)

Arguments

`x`	a numeric vector used for values on the `x`-axis
`major`	major vertical category, e.g., variable labels
`minor`	minor vertical category, e.g. category levels within variables
`group`	superpositioning variable such as treatment
`mult`	strata names for further subdivisions without `group`s
`big`	omit if all levels of `mult` are equally important or if `mult` is omitted. Otherwise denotes major (larger points, right on horizontal lines) vs. minor (smaller, transparent points slightly below the line).
`htext`	additional hover text per point
`num`	if `x` represents proportions, optionally specifies numerators to be used in fractions added to hover text. When `num` is given, `x` is automatically added to hover text, rounded to 3 digits after the decimal point.
`denom`	like `num` but for denominators
`numlabel`	character string to put to the right of the numerator in hover text
`denomlabel`	character string to put to the right of the denominator in hover text
`fun`	a transformation to make when printing estimates. For example, one may specify `fun=exp` to anti-log estimates and confidence limites that were computed on a log basis
`ifun`	inverse transformation of `fun`
`op`	set to for example `'/'` when `fun=exp` and effects are computed as ratios instead of differences. This is used in hover text.
`lower`	lower limits for optional error bars
`upper`	upper limits for optional error bars
`refgroup`	if `group` is specified and there are exactly two groups, specify the character string for the reference group in computing difference in proportions. For example if `refgroup='A'` and the `group` levels are `'A','B'`, you will get B - A.
`sortdiff`	`minor` categories are sorted by descending values of the difference in proportions when `refgroup` is used, unless you specify `sortdiff=FALSE`
`conf.int`	confidence level for computing confidence intervals for the difference in two proportions. Specify `conf.int=FALSE` to suppress confidence intervals.
`minkeep`	if `refgroup` and `minkeep` are both given, observations that are at or above `minkeep` for at least one of the groups are retained. The defaults to to keep all observations.
`xlim`	`x`-axis limits
`xlab`	`x`-axis label
`tracename`	`plotly` trace name if `group` is not used
`limitstracename`	`plotly` trace name for `lower` and `upper` if `group` is not used
`nonbigtracename`	`plotly` trace name used for non-big elements, which usually represent stratified versions of the "big" observations
`col`	a function or vector of colors to assign to `group`. If a function it will be evaluated with an argument equal to the number of distinct groups.
`dec`	number of places to the right of the decimal place for formatting numeric quantities in hover text
`width`	width of plot in pixels
`height`	height of plot in pixels; computed from number of strata by default

Value

a plotly object. An attribute levelsRemoved is added if minkeep is used and any categories were omitted from the plot as a result. This is a character vector with categories removed. If major is present, the strings are of the form major:minor

Author(s)

Frank Harrell

Examples

## Not run: 
set.seed(1)
d <- expand.grid(major=c('Alabama', 'Alaska', 'Arkansas'),
                 minor=c('East', 'West'),
                 group=c('Female', 'Male'),
                 city=0:2)
n <- nrow(d)
d$num   <- round(100*runif(n))
d$denom <- d$num + round(100*runif(n))
d$x     <- d$num / d$denom
d$lower <- d$x - runif(n)
d$upper <- d$x + runif(n)

with(d,
 dotchartpl(x, major, minor, group, city, lower=lower, upper=upper,
            big=city==0, num=num, denom=denom, xlab='x'))

# Show half-width confidence intervals for Female - Male differences
# after subsetting the data to have only one record per
# state/region/group
d <- subset(d, city == 0)
with(d,
 dotchartpl(x, major, minor, group, num=num, denom=denom,
            lower=lower, upper=upper, refgroup='Male')
)

n <- 500
set.seed(1)
d <- data.frame(
  race         = sample(c('Asian', 'Black/AA', 'White'), n, TRUE),
  sex          = sample(c('Female', 'Male'), n, TRUE),
  treat        = sample(c('A', 'B'), n, TRUE),
  smoking      = sample(c('Smoker', 'Non-smoker'), n, TRUE),
  hypertension = sample(c('Hypertensive', 'Non-Hypertensive'), n, TRUE),
  region       = sample(c('North America','Europe','South America',
                          'Europe', 'Asia', 'Central America'), n, TRUE))

d <- upData(d, labels=c(race='Race', sex='Sex'))

dm <- addMarginal(d, region)
s <- summaryP(race + sex + smoking + hypertension ~
                region + treat,  data=dm)

s$region <- ifelse(s$region == 'All', 'All Regions', as.character(s$region))

with(s, 
 dotchartpl(freq / denom, major=var, minor=val, group=treat, mult=region,
            big=region == 'All Regions', num=freq, denom=denom)
)

s2 <- s[- attr(s, 'rows.to.exclude1'), ]
with(s2, 
     dotchartpl(freq / denom, major=var, minor=val, group=treat, mult=region,
                big=region == 'All Regions', num=freq, denom=denom)
)
# Note these plots can be created by plot.summaryP when options(grType='plotly')

# Plot hazard rates and ratios with confidence limits, on log scale
d <- data.frame(tx=c('a', 'a', 'b', 'b'),
                event=c('MI', 'stroke', 'MI', 'stroke'),
                count=c(10, 5, 5, 2),
                exposure=c(1000, 1000, 900, 900))
# There were no zero event counts in this dataset.  In general we
# want to handle that, hence the 0.5 below
d <- upData(d, hazard = pmax(0.5, count) / exposure,
               selog  = sqrt(1. / pmax(0.5, count)),
               lower  = log(hazard) - 1.96 * selog,
               upper  = log(hazard) + 1.96 * selog)
with(d,
     dotchartpl(log(hazard), minor=event, group=tx, num=count, denom=exposure,
                lower=lower, upper=upper,
                fun=exp, ifun=log, op='/',
                numlabel='events', denomlabel='years',
                refgroup='a', xlab='Events Per Person-Year')
)

## End(Not run)

Hmisc

Harrell Miscellaneous

v4.5-0

GPL (>= 2)

Authors

Frank E Harrell Jr <fh@fharrell.com>, with contributions from Charles Dupont and many others.

Initial release

2021-02-27