Plotting options

Introduction

This package provides functions to create an incidence or prevalence plot. There are a couple of options that can be specified when creating such a plot. In this vignette we are using the options in the plotIncidence function, however these same options can be specified in the plotPrevalence function.

cdm <- mockIncidencePrevalence(
  sampleSize = 10000,
  outPre = 0.5
)
#> Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
#>  target signature 'duckdb_connection#Id'.
#>  "duckdb_connection#ANY" would also be valid

cdm <- generateDenominatorCohortSet(
  cdm = cdm, name = "denominator",
  cohortDateRange = c(as.Date("2008-01-01"), as.Date("2012-01-01")),
  sex = c("Male", "Female")
)
#> ℹ Creating denominator cohorts
#> ✔ Cohorts created in 0 min and 3 sec

inc <- estimateIncidence(
  cdm = cdm,
  denominatorTable = "denominator",
  outcomeTable = "outcome",
  interval = "years"
)
#> Getting incidence for analysis 1 of 2
#> Getting incidence for analysis 2 of 2
#> Overall time taken: 0 mins and 2 secs

Faceted plot

This is the default incidence plot where the plot has been faceted by sex.

plotIncidence(inc, facet = "denominator_sex")

Faceted plot - with lines

This is the previous plot where the dots are connected.

plotIncidence(inc, facet = "denominator_sex", ribbon = TRUE)

Faceted plot - with lines, no confidence interval

This is the previous plot where the dots are connected but no confidence interval is shown.

plotIncidence(inc, facet = "denominator_sex", ribbon = TRUE, 
              options = list('hideConfidenceInterval' = TRUE))

Faceted plot - with lines, no confidence interval, stacked, free scales

This is the previous plot where the subplots are shown on top of each other. The facetNcols variable defines the number of columns of the subplots. In addition we set facetScales as “free” so that the axis can vary by facet.

plotIncidence(inc, facet = "denominator_sex", ribbon = TRUE, 
              options = list('point' = FALSE,
                             'facetNcols' = 1, 
                             'facetScales' = "free"))

More plot options

To know which other options are available to customise plots refer to the function optionsPlot(). The description provides a brief explanation on each of the options.

optionsPlot()
#> $hideConfidenceInterval
#> [1] FALSE
#> 
#> $line
#> [1] FALSE
#> 
#> $point
#> [1] TRUE
#> 
#> $facetNcols
#> NULL
#> 
#> $facetScales
#> [1] "fixed"