A plot for the sequence ratios.

It provides a ggplot of the sequence ratios of index and marker cohorts.

Usage

plotSequenceRatios(
  result,
  onlyASR = FALSE,
  plotTitle = NULL,
  labs = c("SR", "Drug Pairs"),
  colours = c("red", "blue"),
  facet = NULL
)

Arguments

result

Table output from summariseSequenceRatios.

onlyASR

If set to be TRUE then only adjusted SR will be plotted. Otherwise if it is set to be FALSE then both adjusted and crude SR will be plotted.

plotTitle

Title of the plot, if NULL no title will be included in the plot.

labs

Axis labels for the plot.

colours

Colours for sequence ratio.

facet

The variable to facet by.

Value

A plot for the sequence ratios of index and marker cohorts.

Examples

# \donttest{
library(CohortSymmetry)
cdm <- mockCohortSymmetry()
#> Warning: ! 9 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `cdm_version` is numeric but expected character
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 2 column in concept do not match expected column type:
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> Warning: ! 3 column in concept_relationship do not match expected column type:
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 3 column in drug_strength do not match expected column type:
#> • `denominator_value` is logical but expected numeric
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> Warning: There are observation period end dates after the current date: 2024-11-29
#> ℹ The latest max observation period end date found is 2026-10-26
#> Warning: There are observation period end dates after the current date: 2024-11-29
#> ℹ The latest max observation period end date found is 2026-10-26
cdm <- generateSequenceCohortSet(cdm = cdm,
                                 indexTable = "cohort_1",
                                 markerTable = "cohort_2",
                                 name = "joined_cohort")
sequence_ratio <- summariseSequenceRatios(cohort = cdm$joined_cohort,
                                          minCellCount = 0)
#> Warning: For at least some combinations, index is always before marker or marker always
#> before index
#> -- 5 combinations of 8 had index always before marker
#> -- 5 combinations of 8 had marker always before index
plotSequenceRatios(result = sequence_ratio)
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_point()`).

CDMConnector::cdmDisconnect(cdm = cdm)
# }